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Schmidt A, Danyel M, Grundmann K, Brunet T, Klinkhammer H, Hsieh TC, Engels H, Peters S, Knaus A, Moosa S, Averdunk L, Boschann F, Sczakiel HL, Schwartzmann S, Mensah MA, Pantel JT, Holtgrewe M, Bösch A, Weiß C, Weinhold N, Suter AA, Stoltenburg C, Neugebauer J, Kallinich T, Kaindl AM, Holzhauer S, Bührer C, Bufler P, Kornak U, Ott CE, Schülke M, Nguyen HHP, Hoffjan S, Grasemann C, Rothoeft T, Brinkmann F, Matar N, Sivalingam S, Perne C, Mangold E, Kreiss M, Cremer K, Betz RC, Mücke M, Grigull L, Klockgether T, Spier I, Heimbach A, Bender T, Brand F, Stieber C, Morawiec AM, Karakostas P, Schäfer VS, Bernsen S, Weydt P, Castro-Gomez S, Aziz A, Grobe-Einsler M, Kimmich O, Kobeleva X, Önder D, Lesmann H, Kumar S, Tacik P, Basin MA, Incardona P, Lee-Kirsch MA, Berner R, Schuetz C, Körholz J, Kretschmer T, Di Donato N, Schröck E, Heinen A, Reuner U, Hanßke AM, Kaiser FJ, Manka E, Munteanu M, Kuechler A, Cordula K, Hirtz R, Schlapakow E, Schlein C, Lisfeld J, Kubisch C, Herget T, Hempel M, Weiler-Normann C, Ullrich K, Schramm C, Rudolph C, Rillig F, Groffmann M, Muntau A, Tibelius A, Schwaibold EMC, Schaaf CP, Zawada M, Kaufmann L, Hinderhofer K, Okun PM, Kotzaeridou U, Hoffmann GF, Choukair D, Bettendorf M, Spielmann M, Ripke A, Pauly M, Münchau A, Lohmann K, Hüning I, Hanker B, Bäumer T, Herzog R, Hellenbroich Y, Westphal DS, Strom T, Kovacs R, Riedhammer KM, Mayerhanser K, Graf E, Brugger M, Hoefele J, Oexle K, Mirza-Schreiber N, Berutti R, Schatz U, Krenn M, Makowski C, Weigand H, Schröder S, Rohlfs M, Vill K, Hauck F, Borggraefe I, Müller-Felber W, Kurth I, Elbracht M, Knopp C, Begemann M, Kraft F, Lemke JR, Hentschel J, Platzer K, Strehlow V, Abou Jamra R, Kehrer M, Demidov G, Beck-Wödl S, Graessner H, Sturm M, Zeltner L, Schöls LJ, Magg J, Bevot A, Kehrer C, Kaiser N, Turro E, Horn D, Grüters-Kieslich A, Klein C, Mundlos S, Nöthen M, Riess O, Meitinger T, Krude H, Krawitz PM, Haack T, Ehmke N, Wagner M. Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings. Nat Genet 2024; 56:1644-1653. [PMID: 39039281 PMCID: PMC11319204 DOI: 10.1038/s41588-024-01836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/18/2024] [Indexed: 07/24/2024]
Abstract
Individuals with ultrarare disorders pose a structural challenge for healthcare systems since expert clinical knowledge is required to establish diagnoses. In TRANSLATE NAMSE, a 3-year prospective study, we evaluated a novel diagnostic concept based on multidisciplinary expertise in Germany. Here we present the systematic investigation of the phenotypic and molecular genetic data of 1,577 patients who had undergone exome sequencing and were partially analyzed with next-generation phenotyping approaches. Molecular genetic diagnoses were established in 32% of the patients totaling 370 distinct molecular genetic causes, most with prevalence below 1:50,000. During the diagnostic process, 34 novel and 23 candidate genotype-phenotype associations were identified, mainly in individuals with neurodevelopmental disorders. Sequencing data of the subcohort that consented to computer-assisted analysis of their facial images with GestaltMatcher could be prioritized more efficiently compared with approaches based solely on clinical features and molecular scores. Our study demonstrates the synergy of using next-generation sequencing and phenotyping for diagnosing ultrarare diseases in routine healthcare and discovering novel etiologies by multidisciplinary teams.
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Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Magdalena Danyel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kathrin Grundmann
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
- Institut für Medizinische Biometrie, Informatik und Epidemiologie, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Shahida Moosa
- Institute for Medical Genetics, Stellenbosch University, Cape Town, South Africa
| | - Luisa Averdunk
- Department of Pediatrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Felix Boschann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sarina Schwartzmann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Atta Mensah
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jean Tori Pantel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Manuel Holtgrewe
- Core Uni Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annemarie Bösch
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Weiß
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Weinhold
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Aude-Annick Suter
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Corinna Stoltenburg
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Neugebauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tillmann Kallinich
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute of Cell and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Holzhauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Bührer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philip Bufler
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claus-Eric Ott
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Schülke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Sabine Hoffjan
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Corinna Grasemann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Tobias Rothoeft
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Folke Brinkmann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Nora Matar
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Sugirthan Sivalingam
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Claudia Perne
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martina Kreiss
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martin Mücke
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Lorenz Grigull
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tim Bender
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Fabian Brand
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Christiane Stieber
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexandra Marzena Morawiec
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pantelis Karakostas
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Valentin S Schäfer
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sarah Bernsen
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Patrick Weydt
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sergio Castro-Gomez
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Ahmad Aziz
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Marcus Grobe-Einsler
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Okka Kimmich
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Xenia Kobeleva
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Demet Önder
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hellen Lesmann
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pawel Tacik
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Meghna Ahuja Basin
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pietro Incardona
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Min Ae Lee-Kirsch
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Reinhard Berner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Catharina Schuetz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Julia Körholz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Tanita Kretschmer
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Nataliya Di Donato
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Evelin Schröck
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - André Heinen
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ulrike Reuner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Neurology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Amalia-Mihaela Hanßke
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Eva Manka
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Martin Munteanu
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Kiewert Cordula
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Raphael Hirtz
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Elena Schlapakow
- Department of Neurology, University Hospital Halle, Halle, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Christina Weiler-Normann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Kurt Ullrich
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Cornelia Rudolph
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Rillig
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Groffmann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ania Muntau
- Department of Pediatrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Michal Zawada
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Pamela M Okun
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Urania Kotzaeridou
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Annekatrin Ripke
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Martje Pauly
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute for Neurogenetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Alexander Münchau
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Irina Hüning
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Britta Hanker
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias Bäumer
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Rebecca Herzog
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Yorck Hellenbroich
- Department of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Tim Strom
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Reka Kovacs
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | | | - Riccardo Berutti
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | - Ulrich Schatz
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Martin Krenn
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Neurology, Medical University of Vienna, Wien, Austria
| | - Christine Makowski
- Department of Paediatrics, Adolescent Medicine and Neonatology, München, Germany
| | - Heike Weigand
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Sebastian Schröder
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Meino Rohlfs
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Katharina Vill
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Fabian Hauck
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Ingo Borggraefe
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | | | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Martin Kehrer
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stefanie Beck-Wödl
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holm Graessner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lena Zeltner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Ludger J Schöls
- Department of Neurology, University of Tübingen, Tübingen, Germany
| | - Janine Magg
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andrea Bevot
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Kehrer
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Nadja Kaiser
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Christoph Klein
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Heiko Krude
- Berlin Centre for Rare Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany.
| | - Tobias Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
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Sandran NG, Fornarino DL, Corbett MA, Kroes T, Gardner AE, MacLennan AH, Gécz J, van Eyk CL. Application of multiple mosaic callers improves post-zygotic mutation detection from exome sequencing data. Genet Med 2024; 26:101220. [PMID: 39041334 DOI: 10.1016/j.gim.2024.101220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
PURPOSE The gold standard for identification of post-zygotic variants (PZVs) is droplet digital polymerase chain reaction or high-depth sequencing across multiple tissues types. These approaches are yet to be systematically implemented for monogenic disorders. We developed PZV detection pipelines for correct classification of de novo variants. METHOD Our pipelines detect PZV in parents (gonosomal mosaicism [pGoM]) and children (somatic mosaicism, "M3"). We applied them to research exome sequencing (ES) data from the Australian Cerebral Palsy Biobank (n = 145 trios) and Simons Simplex Collection (n = 405 families). Candidate mosaic variants were validated using deep amplicon sequencing or droplet digital polymerase chain reaction. RESULTS 69.2% (M3trio), 63.9% (M3single), and 92.7% (pGoM) of detected variants were validated, with 48.6%, 56.7%, and 26.2% of variants, respectively, meeting strict criteria for mosaicism. In the Australian Cerebral Palsy Biobank, 16.6% of probands and 20.7% of parents had at least 1 true-positive somatic or pGoM variant, respectively. A large proportion of PZVs detected in Simons Simplex Collection parents (79.8%) and child (94.5%) were not previously reported. We reclassified 3.7% to 8.0% of germline de novo variants as mosaic. CONCLUSION Many PZVs were incorrectly classified as germline variants or missed by previous approaches. Systematic application of our pipelines could increase genetic diagnostic rate, improve estimates of recurrence risk in families, and benefit novel disease gene identification.
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Affiliation(s)
- Nandini G Sandran
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Dani L Fornarino
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Mark A Corbett
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Thessa Kroes
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Alison E Gardner
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Alastair H MacLennan
- Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gécz
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
| | - Clare L van Eyk
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
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Lecoquierre F, Cassinari K, Drouot N, May A, Fourneaux S, Charbonnier F, Derambure C, Coutant S, Saugier-Veber P, Hoischen A, Charbonnier C, Nicolas G. Assessment of parental mosaicism rates in neurodevelopmental disorders caused by apparent de novo pathogenic variants using deep sequencing. Sci Rep 2024; 14:5289. [PMID: 38438430 PMCID: PMC10912112 DOI: 10.1038/s41598-024-53358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes. We collected 189 patients with NDD-associated DNV. We applied a smMIP enrichment method and sequenced parental blood DNA samples to an average depth of 7000x. Power simulation indicated that mosaicism with an allelic fraction of 0.5% would have been detected for 87% of positions with 90% power. We observed seven parental mosaic variants (3.7% of families), of which four (2.1% of families) had an allelic fraction of less than 1%. In total, our study identifies a relatively low proportion of parental mosaicism in NDD-associated DNVs and raises the question of a biological mechanism behind the higher rates of parental mosaicism detected in other studies, particularly those focusing on epileptic syndromes.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France.
- Centre de Ressources Biologiques institutionnel du CHU de Rouen - Biothèque filière génétique, Rouen, France.
| | - Kévin Cassinari
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Angèle May
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Francoise Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Celine Derambure
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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5
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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6
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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7
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Kim SH, Kwon SS, Park MR, Lee HA, Kim JH, Cha J, Kim S, Baek ST, Kim SH, Lee JS, Kim HD, Choi JR, Lee ST, Kang HC. Detecting low-variant allele frequency mosaic pathogenic variants of NF1, TSC2, and AKT3 genes from blood in patients with neurodevelopmental disorders. J Mol Diagn 2023:S1525-1578(23)00080-6. [PMID: 37088138 DOI: 10.1016/j.jmoldx.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023] Open
Abstract
Growing evidence indicates that early, and late postzygotic mosaicism can cause neurodevelopmental disorders (NDD), but detection of low variant allele frequency (VAF) mosaic variants from blood remains a challenge. We reviewed data of 2,162 patients with NDDs who underwent conventional genetic tests and performed a deep sequencing using specifically designed mosaic NGS panel in the patients with negative genetic test results. Forty-four patents with neurocutaneous syndrome, malformation of cortical development or nonlesional epileptic encephalopathies were included. In total, mosaic variants were detected from blood in 1.2% (25/2,162) of the patients. Using conventional NGS panels, 22 mosaic variants (VAF 8.8-29.8%) were identified in 18 different genes including TSC2, DCX, SLC2A1, PCDH19, DNM1, STXBP1, SCN2A, SCN1A, PURA, POGZ, PAFAH1B1, NF1, KIF21A, KCNQ2, GABRA1, EEF1A2, CDKL5, and ARID1B. Using a specifically designed mosaicism NGS panel, three mosaic variants of the NF1, TSC2, and AKT3 genes were identified (VAF 2.0-11.2%). Mosaic variants were found frequently in the patients who had neurocutaneous syndrome (2/7, 28.6%) whereas only one or no mosaic variant was detected for patients who had malformations of cortical development (1/20, 5%) or nonlesional epileptic encephalopathies (0%, 0/17). In summary, mosaic variants contribute to spectrum of NDDs can be detected from blood via the conventional NGS and specifically designed mosaicism NGS panels, and detection of mosaic variants using blood will increase diagnostic yield.
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Affiliation(s)
- Se Hee Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyeon Ah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hun Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - JiHoon Cha
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Tae Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Soo Lee
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Heung Dong Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Dxome, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Dxome, Seoul, Republic of Korea.
| | - Hoon-Chul Kang
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea.
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8
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Steensma MJ, Lee YL, Bouwman AC, Pita Barros C, Derks MFL, Bink MCAM, Harlizius B, Huisman AE, Crooijmans RPMA, Groenen MAM, Mulder HA, Rochus CM. Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing. BMC Genomics 2023; 24:208. [PMID: 37072725 PMCID: PMC10114323 DOI: 10.1186/s12864-023-09296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. RESULTS We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. CONCLUSIONS Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.
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Affiliation(s)
- Marije J Steensma
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands.
| | - Y L Lee
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - A C Bouwman
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C Pita Barros
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M F L Derks
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - M C A M Bink
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - B Harlizius
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - A E Huisman
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M A M Groenen
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - H A Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C M Rochus
- University of Guelph, Centre for Genetic Improvement of Livestock, 50 Stone Rd E, Guelph, O N, N1G 2W1, Canada
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9
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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10
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia. RESEARCH SQUARE 2023:rs.3.rs-2628288. [PMID: 36909564 PMCID: PMC10002829 DOI: 10.21203/rs.3.rs-2628288/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C . Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5%-37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the rare phenomenon of hypermutation. Eight-hundred-thirty apparent dnSNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component with an average VAF of 25% (range: 18.7-37.41%) (n=446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range: 9.55-18.69%) (n=384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA, and pregnancy loss in general. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics, Houston, TX
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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11
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Bernkopf M, Abdullah UB, Bush SJ, Wood KA, Ghaffari S, Giannoulatou E, Koelling N, Maher GJ, Thibaut LM, Williams J, Blair EM, Kelly FB, Bloss A, Burkitt-Wright E, Canham N, Deng AT, Dixit A, Eason J, Elmslie F, Gardham A, Hay E, Holder M, Homfray T, Hurst JA, Johnson D, Jones WD, Kini U, Kivuva E, Kumar A, Lees MM, Leitch HG, Morton JEV, Németh AH, Ramachandrappa S, Saunders K, Shears DJ, Side L, Splitt M, Stewart A, Stewart H, Suri M, Clouston P, Davies RW, Wilkie AOM, Goriely A. Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation. Nat Commun 2023; 14:853. [PMID: 36792598 PMCID: PMC9932158 DOI: 10.1038/s41467-023-36606-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Following the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1-2% is frequently quoted due to the possibility of parental germline mosaicism; but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)-that could be quantified in semen for paternal cases (recurrence risks of 5.6-12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.
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Affiliation(s)
- Marie Bernkopf
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ummi B Abdullah
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Stephen J Bush
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Katherine A Wood
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sahar Ghaffari
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Geoffrey J Maher
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Loïc M Thibaut
- Centre for Population Genomics, Garvan Institute of Medical Research, UNSW Sydney, Sydney, NSW, Australia
| | - Jonathan Williams
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Edward M Blair
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Fiona Blanco Kelly
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angela Bloss
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Burkitt-Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Natalie Canham
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Alexander T Deng
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Abhijit Dixit
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jacqueline Eason
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Alice Gardham
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Northwick Park Hospital, Harrow, UK
| | - Eleanor Hay
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Muriel Holder
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Jane A Hurst
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Wendy D Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Kivuva
- Clinical Genetics, Royal Devon & Exeter Hospital (Heavitree), Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Melissa M Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Harry G Leitch
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Andrea H Németh
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Shwetha Ramachandrappa
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Katherine Saunders
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton, UK
| | - Miranda Splitt
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Alison Stewart
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mohnish Suri
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Penny Clouston
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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12
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Wood KA, Goriely A. The impact of paternal age on new mutations and disease in the next generation. Fertil Steril 2022; 118:1001-1012. [PMID: 36351856 PMCID: PMC10909733 DOI: 10.1016/j.fertnstert.2022.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Advanced paternal age is associated with an increased risk of fathering children with genetic disorders and other adverse reproductive consequences. However, the mechanisms underlying this phenomenon remain largely unexplored. In this review, we focus on the impact of paternal age on de novo mutations that are an important contributor to genetic disease and can be studied both indirectly through large-scale sequencing studies and directly in the tissue in which they predominantly arise-the aging testis. We discuss the recent data that have helped establish the origins and frequency of de novo mutations, and highlight experimental evidence about the close link between new mutations, parental age, and genetic disease. We then focus on a small group of rare genetic conditions, the so-called "paternal age effect" disorders that show a strong association between paternal age and disease prevalence, and discuss the underlying mechanism ("selfish selection") and implications of this process in more detail. More broadly, understanding the causes and consequences of paternal age on genetic risk has important implications both for individual couples and for public health advice given that the average age of fatherhood is steadily increasing in many developed nations.
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Affiliation(s)
- Katherine A Wood
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Anne Goriely
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom.
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13
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Zakharova V, Raykina E, Mersiyanova I, Deordieva E, Pershin D, Vedmedskia V, Rodina Y, Kuzmenko N, Maschan M, Shcherbina A. Cancer-causing MAP2K1 mutation in a mosaic patient with cardio-facio-cutaneous syndrome and immunodeficiency. Hum Mutat 2022; 43:1852-1855. [PMID: 36054331 DOI: 10.1002/humu.24463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023]
Abstract
RASopathies are disorders caused by germline mutations in genes that encode components of the RAS/mitogen-activated protein kinase (MAPK) pathway. These syndromes share features of developmental delay, facial dysmorphisms, and defects in various organs, as well as cancer predisposition. Somatic mutations of the same pathway are one of the primary causes of cancer. It is thought that germline cancer-causing mutations would be embryonic lethal, as a more severe phenotype was shown in Drosophila and zebrafish embryos with cancer MAP2K1 mutations than in those with RASopathy mutations. Here we report the case of a patient with RASopathy caused by a cancer-associated MAP2K1 p.Phe53Leu mutation. The postzygotic mosaic nature of this mutation could explain the patient's survival.
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Affiliation(s)
- Victorya Zakharova
- Clinical Data Analysis Department, National Medical Research Center for Endocrinology, Moscow, Russian Federation
| | - Elena Raykina
- Laboratory of Molecular Biology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Irina Mersiyanova
- Laboratory of Molecular Biology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Ekaterina Deordieva
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Dmitry Pershin
- Laboratory of Transplant Immunology and Immunotherapy of Hemoblastosis, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Victorya Vedmedskia
- Laboratory of Transplant Immunology and Immunotherapy of Hemoblastosis, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Rodina
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Natalia Kuzmenko
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Michael Maschan
- High School of Molecular and Experimental Medicine, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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14
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Bai Y, Sun Y, Liu N, Wang L, Jiao Z, Hou Y, Duan H, Li Q, Zhu X, Meng J, Kong X. Genetic analysis of 55 cases with fetal skeletal dysplasia. Orphanet J Rare Dis 2022; 17:410. [PMID: 36352425 PMCID: PMC9648031 DOI: 10.1186/s13023-022-02559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Fetal skeletal dysplasia (SD) is a common congenital disability comprising a complex group of skeletal disorders with substantial clinical and genetic heterogeneity. Many of these defects are detected prenatally using ultrasound (US). However, the diagnostic accuracy of the US is limited. METHODS We recruited 55 unrelated fetuses with US-detected skeletal anomalies and performed sequential tests using copy number variation sequencing, targeted skeletal gene panel sequencing, or whole exome sequencing. The detected variants were validated using Sanger sequencing or multiplex ligation-dependent probe amplification. We conducted breakpoint analysis and structural modeling of variants possibly involved in fetal SD. RESULTS A definitive diagnosis was achieved in 81.82% of affected fetuses (45/55). We identified chromosomal abnormalities in seven cases and 36 variants, of which 18 were novel pathogenic or likely pathogenic in 11 genes in 38 cases. De novo variants were identified in 27 cases (71.05%, 27/38), and one gonosomal mosaicism variant was found in the mother of one fetus. Our case examples demonstrated the high heterogeneity of fetal SDs and the rare fetal SD-associated challenges. CONCLUSIONS Careful clinical evaluation of fetuses with SD can guide appropriate molecular testing. Our study extends the SD-associated pathogenic variant spectrum and provides useful genetic counselling guidance and an accurate prenatal diagnosis strategy.
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Affiliation(s)
- Ying Bai
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yue Sun
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ning Liu
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Li Wang
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Zhihui Jiao
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yaqin Hou
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Huikun Duan
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Qianqian Li
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaofan Zhu
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Jingjing Meng
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiangdong Kong
- grid.412633.10000 0004 1799 0733Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
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15
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Kuroda Y, Ritter A, Mullegama SV, Izumi K. Mosaic RAI1 variant in a Smith-Magenis syndrome patient with total anomalous pulmonary venous return. Am J Med Genet A 2022; 188:3130-3134. [PMID: 35833697 DOI: 10.1002/ajmg.a.62907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/23/2022] [Accepted: 06/30/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Yukiko Kuroda
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alyssa Ritter
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Kosuke Izumi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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16
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Willard N, Abman SH, Galambos C, Kinsella JP, Stankiewicz P. High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV. Mol Genet Genomic Med 2022; 10:e2062. [PMID: 36124617 PMCID: PMC9651602 DOI: 10.1002/mgg3.2062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) results from haploinsufficiency of the mesenchymal transcription factor FOXF1 gene. To date, only one case of an ACDMPV-causative CNV deletion inherited from a very-low level somatic mosaic mother has been reported. METHODS Clinical, histopathological, and molecular studies, including whole genome sequencing, chromosomal microarray analysis, qPCR, and Sanger sequencing, followed by in vitro fertilization (IVF) with preimplantation genetic testing (PGT) were used to study a family with a deceased neonate with ACDMPV. RESULTS A pathogenic CNV deletion of the lung-specific FOXF1 enhancer in the proband was found to be inherited from an unaffected mother, 36% mosaic for this deletion in her peripheral blood cells. The qPCR analyses of saliva, buccal cells, urine, nail, and hair samples revealed 19%, 18%, 15%, 19%, and 27% variant allele fraction, respectively, indicating a high recurrence risk. Grandparental studies revealed that the deletion arose on the mother's paternal chromosome 16. PGT studies revealed 44% embryos with the deletion, reflecting high-level germline mosaicism. CONCLUSION Our data further demonstrate the importance of parental testing in ACDMPV families and reproductive usefulness of IVF with PGT in families with high-level parental gonosomal mosaicism.
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Affiliation(s)
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical MicrobiologyPoznan University of Medical SciencesPoznanPoland
| | | | - Tomasz Gambin
- Institute of Computer ScienceWarsaw University of TechnologyWarsawPoland
| | - Nicholas Willard
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Steven H. Abman
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Csaba Galambos
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA,Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - John P. Kinsella
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Paweł Stankiewicz
- Department of Molecular & Human GeneticsBaylor College of MedicineHoustonTexasUSA
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17
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Shi S, Wang Q, Shang Y, Bu C, Lu M, Jiang M, Zhang H, Yu S, Zeng J, Zhang Z, Du Z, Xiao J. TSomVar: a tumor-only somatic and germline variant identification method with random forest. Brief Bioinform 2022; 23:6695269. [DOI: 10.1093/bib/bbac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.
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Affiliation(s)
- Shuo Shi
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Burning Rock Biotech Ltd , Shanghai 201114, China
| | - Qi Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Qujiang Culture Finance Holding (Group) Co., Ltd , Xian 710061, China
| | - Yunfei Shang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Meiye Jiang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Hao Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shuhuan Yu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Zaichao Zhang
- Department of Biology, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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18
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Herzig AF, Clerget-Darpoux F, Génin E. The False Dawn of Polygenic Risk Scores for Human Disease Prediction. J Pers Med 2022; 12:jpm12081266. [PMID: 36013215 PMCID: PMC9409868 DOI: 10.3390/jpm12081266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Polygenic risk scores (PRSs) are being constructed for many diseases and are presented today as a promising avenue in the field of human genetics. These scores aim at predicting the risk of developing a disease by leveraging the many genome-wide association studies (GWAS) conducted during the two last decades. Important investments are being made to improve score estimates by increasing GWAS sample sizes, by developing more sophisticated methods, and by proposing different corrections for potential biases. PRSs have entered the market with direct-to-consumer companies proposing to compute them from saliva samples and even recently to help parents select the healthiest embryos. In this paper, we recall how PRSs arose and question the credit they are given by revisiting underlying assumptions in light of the history of human genetics and by comparing them with estimated breeding values (EBVs) used for selection in livestock.
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Affiliation(s)
- Anthony F. Herzig
- Inserm, Université de Brest, EFS, CHU Brest, UMR 1078, GGB, F-29200 Brest, France;
| | - Françoise Clerget-Darpoux
- Université Paris Cité, Inserm, Institut Imagine, Laboratoire Embryologie et Génétique des Malformations, F-75015 Paris, France
- Correspondence: (F.C.-D.); (E.G.)
| | - Emmanuelle Génin
- Inserm, Université de Brest, EFS, CHU Brest, UMR 1078, GGB, F-29200 Brest, France;
- Correspondence: (F.C.-D.); (E.G.)
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19
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Non-Invasive Detection of a De Novo Frameshift Variant of STAG2 in a Female Fetus: Escape Genes Influence the Manifestation of X-Linked Diseases in Females. J Clin Med 2022; 11:jcm11144182. [PMID: 35887945 PMCID: PMC9323000 DOI: 10.3390/jcm11144182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/01/2023] Open
Abstract
Background: We report on a 20-week-old female fetus with a diaphragmatic hernia and other malformations, all of which appeared after the first-trimester ultrasound. Methods and Results: Whole trio exome sequencing (WES) on cell-free fetal DNA (cff-DNA) revealed a de novo frameshift variant of the X-linked STAG2 gene. Loss-of-function (LoF) STAG2 variants cause either holoprosencephaly (HPE) or Mullegama–Klein–Martinez syndrome (MKMS), are de novo, and only affect females, indicating male lethality. In contrast, missense mutations associate with milder forms of MKMS and follow the classic X-linked recessive inheritance transmitted from healthy mothers to male offspring. STAG2 has been reported to escape X-inactivation, suggesting that disease onset in LoF females is dependent on inadequate dosing for at least some of the transcripts, as is the case with a part of the autosomal dominant diseases. Missense STAG2 variants produce a quantity of transcripts, which, while resulting in a different protein, leads to disease only in hemizygous males. Similar inheritance patterns are described for other escapee genes. Conclusions: This study confirms the advantage of WES on cff-DNA and emphasizes the role of the type of the variant in X-linked disorders.
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20
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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21
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Lee M, Lui ACY, Mak CCY, Tsang MHY, Fung JLF, Yeung KS, Chung BHY. Clinical implications of mosaicism: a 10-year retrospective review of 83 families in a university-affiliated genetics clinic. Clin Dysmorphol 2022; 31:113-124. [PMID: 35256561 DOI: 10.1097/mcd.0000000000000418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mosaicism refers to the coexistence of two or more genetically distinct cell populations in an individual from a single fertilized egg. We performed a retrospective analysis of all patients diagnosed with mosaic disorders between 2010 and 2021 in a university-affiliated genetics clinic, which attends to territory-wide genetic consultations. All patients with confirmed mosaic diagnoses through reproductive (n = 6), prenatal (n = 24), and postnatal (n = 53) testing were examined. We observed that mosaic 45, X (n = 31) and PIK3CA-related overgrowth spectrum (n = 16) disorders were among the most prevalent diagnoses in the clinic, and the total percentage of patients with mosaicism in our cohort was 2.0% (83/4157). A review of the diagnostic journey highlights the challenge in diagnosing mosaic disorders, whereby 38% of the subjects required more than one test sample, and 52% of the cases required more than one orthogonal method of detection to reach the correct diagnosis. While detection of mosaicism is passive through routine clinical testing, for example karyotyping in reproductive and prenatal care, in postnatal care, clinicians can more actively drive the detection of mosaicism. Therefore, we recommend a low threshold for additional genetic testing in suspected mosaicism for more accurate diagnosis and counselling.
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Affiliation(s)
- Mianne Lee
- School of Clinical Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
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22
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Montano C, Britton JF, Harris JR, Kerkhof J, Barnes BT, Lee JA, Sadikovic B, Sobreira N, Fahrner JA. Genome-wide DNA methylation profiling confirms a case of low-level mosaic Kabuki syndrome 1. Am J Med Genet A 2022; 188:2217-2225. [PMID: 35384273 PMCID: PMC9321966 DOI: 10.1002/ajmg.a.62754] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/22/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022]
Abstract
Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.
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Affiliation(s)
- Carolina Montano
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Benjamin T Barnes
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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24
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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25
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Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
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Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
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26
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Domogala DD, Gambin T, Zemet R, Wu CW, Schulze KV, Yang Y, Wilson TA, Machol I, Liu P, Stankiewicz P. Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset. Hum Genomics 2021; 15:72. [PMID: 34930489 PMCID: PMC8686574 DOI: 10.1186/s40246-021-00369-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. METHODS Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). RESULTS In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. CONCLUSIONS Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.
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Affiliation(s)
- Daniel D Domogala
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas at MD Anderson, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chung Wah Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- AiLife Diagnostics, 1920 Country Place Pkwy Suite 100, Pearland, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,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.
| | - Maria João Nabais Sá
- 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
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,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
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28
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Liu B, Chen M, Yang Y, Huang Y, Qian Y, Dong M. Identification of of a PAX2 mutation from maternal mosaicism causes recurrent renal disorder in siblings. Clin Chim Acta 2021; 525:23-28. [PMID: 34906559 DOI: 10.1016/j.cca.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND PAX2-related disorder is an autosomal dominant disorder characterized by renal and eye abnormalities. Some patients may present with isolated renal abnormalities without obvious ocular abnormalities. It is associated with mutations in paired box gene 2 (PAX2), which is one of the families of paired box transcription factor genes. Studies on mosaicism have been limited in PAX2-related disorder, as only three families with mosaic PAX2 mutations have been reported in the literature. METHODS The proband with multicystic dysplastic kidneys from a Chinese family was recruited in our study. Detailed clinical symptoms were enquired. Trio-based whole exome sequencing (WES), SNP array, sanger sequencing and droplet digital PCR (ddPCR) were used to characterize etiology in the proband. Prenatal diagnosis was performed through amniocentesis and prenatal ultrasound when the proband's mother was further pregnant at 20 weeks. RESULTS A heterozygous missense mutation in PAX2 (c.194 T > C) was identified in the proband. His asymptomatic mother has the same mutation with somatic mosaicism ratio of 22%. The mutation was also detected in the fetus. Prenatal ultrasound showed that bilateral hyperechogenic kidneys with decrease of renal size. CONCLUSIONS This is the first report on PAX2 mosaicism in a Chinese family. Identifying PAX2 mosaicism provides more evidence for estimating recurrence risk. Our findings have important implications on genetic counseling for patients with PAX2-related disorder and provide an effective diagnostic technology for mosaicism.
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Affiliation(s)
- Bei Liu
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Mengjia Chen
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yanmei Yang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yingzhi Huang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yeqing Qian
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Minyue Dong
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China.
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29
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Muirhead KJ, Clause AR, Schlachetzki Z, Dubbs H, Perry DL, Hagelstrom RT, Taft RJ, Vanderver A. Genome sequencing identifies three molecular diagnoses including a mosaic variant in the COL2A1 gene in an individual with Pol III-related leukodystrophy and Feingold syndrome. Cold Spring Harb Mol Case Stud 2021; 7:a006143. [PMID: 34737199 PMCID: PMC8751417 DOI: 10.1101/mcs.a006143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
Undiagnosed genetic disease imposes a significant burden on families and health-care resources, especially in cases with a complex phenotype. Here we present a child with suspected leukodystrophy in the context of additional features, including hearing loss, clinodactyly, rotated thumbs, tapered fingers, and simplified palmar crease. Trio genome sequencing (GS) identified three molecular diagnoses in this individual: compound heterozygous missense variants associated with polymerase III (Pol III)-related leukodystrophy, a 4-Mb de novo copy-number loss including the MYCN gene associated with Feingold syndrome, and a mosaic single-nucleotide variant associated with COL2A1-related disorders. These variants fully account for the individual's features, but also illustrate the potential for superimposed and unclear contributions of multiple diagnoses to an individual's overall presentation. This report demonstrates the advantage of GS in detection of multiple variant types, including low-level mosaic variants, and emphasizes the need for comprehensive genetic analysis and detailed clinical phenotyping to provide individuals and their families with the maximum benefit for clinical care and genetic counseling.
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Affiliation(s)
- Kayla J Muirhead
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Amanda R Clause
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, California 92122, USA
| | - Zinayida Schlachetzki
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, California 92122, USA
| | - Holly Dubbs
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Denise L Perry
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, California 92122, USA
| | - R Tanner Hagelstrom
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, California 92122, USA
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, California 92122, USA
| | - Adeline Vanderver
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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30
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Melas M, Mathew MT, Mori M, Jayaraman V, Wilson SA, Martin C, Jacobson-Kelly AE, Kelly BJ, Magrini V, Mardis ER, Cottrell CE, Lee K. Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006135. [PMID: 34716204 PMCID: PMC8751410 DOI: 10.1101/mcs.a006135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-mo-old male who presented with profound global delays, brain abnormality, progressive microcephaly, and growth deficiency, as well as metopic craniosynostosis. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G > A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T > C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome–like disorder with or without juvenile myelomonocytic leukemia. Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Mariam T Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State Univ; Dept of Pediatrics, The Ohio State University
| | - Mari Mori
- Dept of Pediatrics, The Ohio State University; Genetic and Genomic Medicine, Nationwide Children's Hospital
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Sarah A Wilson
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | | | - Amanda E Jacobson-Kelly
- Dept of Pediatrics, The Ohio State University; Division of Hematology/Oncology/BMT, Nationwide Children's Hospital
| | - Ben J Kelly
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
| | - Kristy Lee
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
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31
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Cook CB, Armstrong L, Boerkoel CF, Clarke LA, du Souich C, Demos MK, Gibson WT, Gill H, Lopez E, Patel MS, Selby K, Abu-Sharar Z, Elliott AM, Friedman JM. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: clinical and genetic counseling implications. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006125. [PMID: 34697084 PMCID: PMC8751411 DOI: 10.1101/mcs.a006125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 01/28/2023] Open
Abstract
Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
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Affiliation(s)
- Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Lorne A Clarke
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Harinder Gill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Elena Lopez
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Millan S Patel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - Ziad Abu-Sharar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4.,Women's Health Research Institute, Vancouver, British Columbia, Canada V6H 2N9
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
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32
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Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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33
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Yan YH, Chen SX, Cheng LY, Rodriguez AY, Tang R, Cabrera K, Zhang DY. Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing. Sci Rep 2021; 11:11640. [PMID: 34079006 PMCID: PMC8172533 DOI: 10.1038/s41598-021-91142-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.
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Affiliation(s)
| | - Sherry X Chen
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | | | - Rui Tang
- NuProbe USA, Inc., Houston, TX, USA
| | | | - David Yu Zhang
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA.
- Systems, Synthetic, and Physical Biology, Rice University, 6500 Main St, Houston, TX, 77030, USA.
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34
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Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2021 update: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1391-1398. [PMID: 34012069 DOI: 10.1038/s41436-021-01171-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022] Open
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35
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Närhi A, Fernandes A, Toiviainen-Salo S, Harris J, McInerney-Leo A, Lazarus S, Avela K, Duncan EL. A family with partially penetrant multicentric carpotarsal osteolysis due to gonadal mosaicism: First reported case. Am J Med Genet A 2021; 185:2477-2481. [PMID: 33988298 DOI: 10.1002/ajmg.a.62257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/17/2021] [Accepted: 04/10/2021] [Indexed: 01/30/2023]
Abstract
Multicentric carpotarsal osteolysis (MCTO) is an autosomal dominant condition characterized by carpal-tarsal abnormalities; over half of affected individuals also develop renal disease. MCTO is caused by mutations of MAFB; however, there is no clear phenotype-genotype correlation. We describe the first reported family of variable MCTO phenotype due to mosaicism: the proband had classical skeletal features and renal involvement due to focal segmental glomerulosclerosis (FSGS), and the father had profound renal impairment due to FSGS, necessitating kidney transplantation. Mosaicism was first suspected in this family due to unequal allele ratios in the sequencing chromatograph of the initial blood sample of proband's father and confirmed by sequencing DNA extracted from the father's hair, collected from different bodily parts. This case highlights the need for a high index of clinical suspicion to detect low-level parental mosaicism, as well as a potential role for MAFB mutation screening in individuals with isolated FSGS.
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Affiliation(s)
- Anu Närhi
- Department of Clinical Genetics, Helsinki University Hospital, Helenski, Finland
| | - Andrea Fernandes
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Herston, Australia.,Faculty of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Faculty of Medicine, Herston, University of Queensland, Herston, Australia
| | - Sanna Toiviainen-Salo
- Department of Radiology, New Children's Hospital, Helsinki University Hospital, Helenski, Finland
| | - Jessica Harris
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Australia
| | - Aideen McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Australia
| | - Syndia Lazarus
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Herston, Australia.,Faculty of Medicine, Herston, University of Queensland, Herston, Australia.,Department of Internal Medicine (Endocrinology), The Prince Charles Hospital, Chermside, Australia
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital, Helenski, Finland
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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36
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Shu L, Zhang Q, Tian Q, Yang S, Peng X, Mao X, Yang L, Du J, Wang H. Parental mosaicism in de novo neurodevelopmental diseases. Am J Med Genet A 2021; 185:2119-2125. [PMID: 33851778 DOI: 10.1002/ajmg.a.62174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/28/2021] [Accepted: 02/26/2021] [Indexed: 11/12/2022]
Abstract
Neurodevelopmental diseases are increasingly recognized to be caused by "de novo" variants with the expanding use of next-generation sequencing. The apparent de novo variants may actually be low-level hereditary parental mosaic variants, which could increase the recurrence risk of disease by >50% and is thought to be an underappreciated cause of neurodevelopmental diseases. Our study aimed to investigate the frequency of parental mosaicism in "de novo" neurodevelopmental diseases. A total of 237 patients (and parents) with neurodevelopmental diseases carrying apparent de novo pathogenic or likely pathogenic variants were recruited consecutively. Deep next-generation sequencing was performed on parental samples to identify parental mosaicism. Fourteen parental disease-causing mosaicism variants (3.0%) in 11 genes were detected with alternate allele frequency (AAF) 0.22%-34%. Three parents showed milder clinical phenotypes than their offspring with relatively high AAF (23.33%, 25%, 34% separately). One recurrent variant was identified prenatally. A review of cohort study on parental mosaicism in neurodevelopmental diseases was performed. Our study highlights that identifying the parental mosaic disease-causing variants especially the low-level mosaicism will contribute to improving the accuracy of genetic counseling and prenatal diagnosis for reproductive risks.
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Affiliation(s)
- Li Shu
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Department of School of Life Sciences, Central South University, Changsha, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Qi Tian
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Sai Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Xingwang Peng
- Marketing Management Center, AmCare Genomics Laboratory, Guangzhou, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Liming Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Hua Wang
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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37
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Lin S, He Z, Huang L, Liu J, Lei T, Wu J, Huang P, Zhou Y, Luo Y. Case Report: Low-Level Maternal Mosaicism of a Novel CREBBP Variant Causes Recurrent Rubinstein-Taybi Syndrome in Two Siblings of a Chinese Family. Front Genet 2021; 12:640992. [PMID: 33747050 PMCID: PMC7970026 DOI: 10.3389/fgene.2021.640992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/15/2021] [Indexed: 01/05/2023] Open
Abstract
Familial Rubinstein-Taybi syndrome (RSTS) with recurrent RSTS siblings and apparently unaffected parents is rare; such cases might result from parental somatic and/or germline mosaicism. Parental low-level (<10%) germline mosaicism in the CREBBP-associated RSTS family has not been reported. Here, we present our studies of a Chinese family with two RSTS siblings and apparently unaffected parents. We detected the apparent de novo variant (DNV) c.3235C>T (p.Gln1079*) in CREBBP in the siblings via trio whole-exome sequencing. High-depth next-generation sequencing (NGS) for the parents revealed a low-level (<10%) mosaic variant in both the peripheral blood (3.64%) and buccal mucosa (1.94%) of the unaffected mother, indicating maternal somatic and germline mosaicism. Peripheral blood RNA-sequencing analysis for the patients and normal individuals indicated that the c.3235C>T (p.Gln1079*) non-sense variant did not trigger nonsense-mediated mRNA decay to reduce CREBBP mRNA levels. Transcriptome analysis revealed 151 downregulated mRNAs and 132 upregulated mRNAs between the patients and normal individuals. This study emphasizes that high-depth NGS using multiple specimens might be applied for a family with an affected sibling caused by an apparent CREBBP DNV to identify potential low-level parental mosaicism and provide an assessment of recurrence risk.
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Affiliation(s)
- Shaobin Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiming He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linhuan Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jialiu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ting Lei
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianzhu Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Peizhi Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yi Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanmin Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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38
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Striessnig J. Voltage-Gated Ca 2+-Channel α1-Subunit de novo Missense Mutations: Gain or Loss of Function - Implications for Potential Therapies. Front Synaptic Neurosci 2021; 13:634760. [PMID: 33746731 PMCID: PMC7966529 DOI: 10.3389/fnsyn.2021.634760] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes our current knowledge of human disease-relevant genetic variants within the family of voltage gated Ca2+ channels. Ca2+ channelopathies cover a wide spectrum of diseases including epilepsies, autism spectrum disorders, intellectual disabilities, developmental delay, cerebellar ataxias and degeneration, severe cardiac arrhythmias, sudden cardiac death, eye disease and endocrine disorders such as congential hyperinsulinism and hyperaldosteronism. A special focus will be on the rapidly increasing number of de novo missense mutations identified in the pore-forming α1-subunits with next generation sequencing studies of well-defined patient cohorts. In contrast to likely gene disrupting mutations these can not only cause a channel loss-of-function but can also induce typical functional changes permitting enhanced channel activity and Ca2+ signaling. Such gain-of-function mutations could represent therapeutic targets for mutation-specific therapy of Ca2+-channelopathies with existing or novel Ca2+-channel inhibitors. Moreover, many pathogenic mutations affect positive charges in the voltage sensors with the potential to form gating-pore currents through voltage sensors. If confirmed in functional studies, specific blockers of gating-pore currents could also be of therapeutic interest.
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Affiliation(s)
- Jörg Striessnig
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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39
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Strubbe I, Van Cauwenbergh C, De Zaeytijd J, De Jaegere S, De Bruyne M, Rosseel T, Van de Sompele S, De Baere E, Leroy BP. Phenocopy of a heterozygous carrier of X-linked retinitis pigmentosa due to mosaicism for a RHO variant. Sci Rep 2021; 11:117. [PMID: 33420188 PMCID: PMC7794345 DOI: 10.1038/s41598-020-80400-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
We describe both phenotype and pathogenesis in two male siblings with typical retinitis pigmentosa (RP) and the potentially X-linked RP (XLRP) carrier phenotype in their mother. Two affected sons, two unaffected daughters, and their mother underwent detailed ophthalmological assessments including Goldmann perimetry, color vision testing, multimodal imaging and ISCEV-standard electroretinography. Genetic testing consisted of targeted next-generation sequencing (NGS) of known XLRP genes and whole exome sequencing (WES) of known inherited retinal disease genes (RetNet-WES). Variant validation and segregation analysis were performed by Sanger sequencing. The mutational load of the RHO variant in the mother was assessed in DNA from leucocytes, buccal cells and hair follicles using targeted NGS. Both affected sons showed signs of classical RP, while the mother displayed patches of hyperautofluorescence on blue light autofluorescence imaging and regional, intraretinal, spicular pigmentation, reminiscent of a carrier phenotype of XLRP. XLRP testing was negative. RetNet-WES testing revealed RHO variant c.404G > C p.(Arg135Pro) in a mosaic state (21% of the reads) in the mother and in a heterozygous state in both sons. Targeted NGQSS of the RHO variant in different maternal tissues showed a mutation load between 25.06% and 41.72%. We report for the first time that somatic mosaicism of RHO variant c.404G > C p.(Arg135Pro) mimics the phenotype of a female carrier of XLRP, in combination with heterozygosity for the variant in the two affected sons.
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Affiliation(s)
- Ine Strubbe
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium. .,Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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40
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Moreno-García M, Arteche-López AR, Álvarez-Mora MI, Palma Milla C, Quesada Espinosa JF, Lezana Rosales JM, Sánchez Calvín MT, Gómez Manjón I, Gómez Rodríguez MJ, Mendez-Guerrero A, Villarejo-Galende A. First patient with mosaic NOTCH3 gene pathogenic variant. Unrevealed mosaicisms and importance of their detection. Am J Med Genet A 2020; 185:591-595. [PMID: 33305890 DOI: 10.1002/ajmg.a.61999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/06/2020] [Accepted: 11/14/2020] [Indexed: 01/14/2023]
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited small vessel disease caused predominantly by pathogenic variants in NOTCH3 gene. Neither germline nor somatic mosaicism has been previously published in NOTCH3 gene. CADASIL is inherited in an autosomal dominant manner; only rare cases have been associated with de novo pathogenic variants. Mosaicism is more common than previously thought because mosaic variants often stay unrevealed. An apparently de novo variant might actually be a consequence of a parental mosaicism undetectable with Sanger sequencing, especially in the case of low grade mosaicism. Parental testing by sensitive tools like deep targeted next-generation sequencing (NGS) analysis could detect cases of unrevealed medium or low level mosaicism in patients tested by Sanger sequencing. Here, we report the first patient with mosaic NOTCH3 gene pathogenic variant to our knowledge; the allelic fraction in the leucocyte DNA was low (13%); the pathogenic variant was inhered by his two daughters. The patient was diagnosed by deep targeted NGS analysis after studying his two affected daughters. This report highlights the importance of parental testing by sensitive tools like deep targeted NGS analysis. Detection of mosaicism is of great importance for diagnosis and adequate family genetic counseling.
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Affiliation(s)
| | | | | | - Carmen Palma Milla
- Department of Genetics, University 12 de Octubre Hospital, Madrid, Spain
| | | | | | | | - Irene Gómez Manjón
- Department of Genetics, University 12 de Octubre Hospital, Madrid, Spain
| | | | | | - Alberto Villarejo-Galende
- Department of Neurology, University 12 de Octubre Hospital, Neurodegenerative Diseases Study Group, I+12, CIBERNED, Universidad Complutense, Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
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41
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Cope H, Spillmann R, Rosenfeld JA, Brokamp E, Signer R, Schoch K, Kelley EG, Sullivan JA, Macnamara E, Lincoln S, Golden‐Grant K, Orengo JP, Clark G, Burrage LC, Posey JE, Punetha J, Robertson A, Cogan J, Phillips JA, Martinez‐Agosto J, Shashi V. Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Mol Genet Genomic Med 2020; 8:e1397. [PMID: 32730690 PMCID: PMC7549585 DOI: 10.1002/mgg3.1397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings. METHODS The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data. RESULTS We present 12 participants that illustrate how clinical practices such as phenotype-driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses. CONCLUSION These examples demonstrate that when a diagnosis is elusive, an iterative patient-specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Rebecca Spillmann
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Jill A. Rosenfeld
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Rebecca Signer
- Department of Human GeneticsUniversity of CaliforniaLos AngelesCAUSA
| | - Kelly Schoch
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Emily G. Kelley
- Department of Biomedical InformaticsHarvard Medical SchoolBostonMAUSA
| | - Jennifer A. Sullivan
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Ellen Macnamara
- Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNational Institutes of HealthNIHBethesdaMDUSA
| | - Sharyn Lincoln
- Division of Genetics and GenomicsDepartment of PediatricsBoston Children’s HospitalBostonMAUSA
| | | | | | - James P. Orengo
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Gary Clark
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Lindsay C. Burrage
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jaya Punetha
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Amy Robertson
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Joy Cogan
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - John A. Phillips
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | | | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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42
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Holtgrewe M, Stolpe O, Nieminen M, Mundlos S, Knaus A, Kornak U, Seelow D, Segebrecht L, Spielmann M, Fischer-Zirnsak B, Boschann F, Scholl U, Ehmke N, Beule D. VarFish: comprehensive DNA variant analysis for diagnostics and research. Nucleic Acids Res 2020; 48:W162-W169. [PMID: 32338743 PMCID: PMC7319464 DOI: 10.1093/nar/gkaa241] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.
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Affiliation(s)
- Manuel Holtgrewe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Oliver Stolpe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Mikko Nieminen
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Lara Segebrecht
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Malte Spielmann
- Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.,Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Ute Scholl
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Dieter Beule
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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Mhaske A, Dileep K, Kumar M, Poojary M, Pandhare K, Zhang KY, Scaria V, Binukumar B. ATP7A Clinical Genetics Resource - A comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput Struct Biotechnol J 2020; 18:2347-2356. [PMID: 32994893 PMCID: PMC7501406 DOI: 10.1016/j.csbj.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
ATP7A is a critical copper transporter involved in Menkes Disease, Occipital horn Syndrome and X-linked distal spinal muscular atrophy type 3 which are X linked genetic disorders. These are rare diseases and their genetic epidemiology of the diseases is unknown. A number of genetic variants in the genes have been reported in published literature as well as databases, however, understanding the pathogenicity of variants and genetic epidemiology requires the data to be compiled in a unified format. To this end, we systematically compiled genetic variants from published literature and datasets. Each of the variants were systematically evaluated for evidences with respect to their pathogenicity and classified as per the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG-AMP) guidelines into Pathogenic, Likely Pathogenic, Benign, Likely Benign and Variants of Uncertain Significance. Additional integrative analysis of population genomic datasets provides insights into the genetic epidemiology of the disease through estimation of carrier frequencies in global populations. To deliver a mechanistic explanation for the pathogenicity of selected variants, we also performed molecular modeling studies. Our modeling studies concluded that the small structural distortions observed in the local structures of the protein may lead to the destabilization of the global structure. To the best of our knowledge, ATP7A Clinical Genetics Resource is one of the most comprehensive compendium of variants in the gene providing clinically relevant annotations in gene.
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Affiliation(s)
- Aditi Mhaske
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - K.V. Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kam Y.J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
| | - B.K. Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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45
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When phenotype does not match genotype: importance of "real-time" refining of phenotypic information for exome data interpretation. Genet Med 2020; 23:215-221. [PMID: 32801363 DOI: 10.1038/s41436-020-00938-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Clinical data provided to genetic testing laboratories are frequently scarce. Our purpose was to evaluate clinical scenarios where phenotypic refinement in proband's family members might impact exome data interpretation. METHODS Of 614 exomes, 209 were diagnostic and included in this study. Phenotypic information was gathered by the variant interpretation team from genetic counseling letters and images. If a discrepancy between reported clinical findings and presumably disease-causing variant segregation was observed, referring clinicians were contacted for phenotypic clarification. RESULTS In 16/209 (7.7%) cases, phenotypic refinement was important due to (1) lack of cosegregation of disease-causing variant with the reported phenotype; (2) identification of different disorders with overlapping symptoms in the same family; (3) similar features in proband and family members, but molecular cause identified in proband only; and (4) previously unrecognized maternal condition causative of child's phenotype. As a result of phenotypic clarification, in 12/16 (75%) cases definition of affected versus unaffected status in one of the family members has changed, and in one case variant classification has changed. CONCLUSION Detailed description of phenotypes in family members including differences in clinical presentations, even if subtle, are important in exome interpretation and should be communicated to the variant interpretation team.
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46
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Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 2020; 22:1768-1776. [PMID: 32655138 PMCID: PMC7606563 DOI: 10.1038/s41436-020-0897-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases. Methods: We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents. Results: Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples. Conclusion: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nina G Xie
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ed Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005231. [PMID: 32371413 PMCID: PMC7304353 DOI: 10.1101/mcs.a005231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.
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Affiliation(s)
- Cecelia R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shalini C Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Donald J Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Ashita Dave-Wala
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Daniel Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Theodora Matthews
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Danielle Mouhlas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Maggie Stein
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Tom Grossman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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48
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Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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49
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Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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50
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Highly Sensitive Blocker Displacement Amplification and Droplet Digital PCR Reveal Low-Level Parental FOXF1 Somatic Mosaicism in Families with Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. J Mol Diagn 2020; 22:447-456. [PMID: 32036090 DOI: 10.1016/j.jmoldx.2019.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
Detection of low-level somatic mosaicism [alternate allele fraction (AAF) ≤ 10%] in parents of affected individuals with the apparent de novo pathogenic variants enables more accurate estimate of recurrence risk. To date, only a few systematic analyses of low-level parental somatic mosaicism have been performed. Herein, highly sensitive blocker displacement amplification, droplet digital PCR, quantitative PCR, long-range PCR, and array comparative genomic hybridization were applied in families with alveolar capillary dysplasia with misalignment of pulmonary veins. We screened 18 unrelated families with the FOXF1 variant previously determined to be apparent de novo (n = 14), of unknown parental origin (n = 1), or inherited from a parent suspected to be somatic and/or germline mosaic (n = 3). We identified four (22%) families with FOXF1 parental somatic mosaic single-nucleotide variants (n = 3) and copy number variant deletion (n = 1) detected in parental blood samples and an AAF ranging between 0.03% and 19%. In one family, mosaic allele ratio in tissues originating from three germ layers ranged between <0.03% and 0.65%. Because the ratio of parental somatic mosaicism have significant implications for the recurrence risk, this study further implies the importance of a systematic screening of parental samples for low-level and very-low-level (AAF ≤ 1%) somatic mosaicism using methods that are more sensitive than those routinely applied in diagnostics.
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