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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 2024:10.1038/s41588-024-01836-1. [PMID: 39039281 DOI: 10.1038/s41588-024-01836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Klarić ML, Marić T, Žunić L, Trgovec-Greif L, Rokić F, Fiolić A, Šorgić AM, Ježek D, Vugrek O, Jakovčević A, Barbalić M, Belužić R, Katušić Bojanac A. FANCM Gene Variants in a Male Diagnosed with Sertoli Cell-Only Syndrome and Diffuse Astrocytoma. Genes (Basel) 2024; 15:707. [PMID: 38927643 PMCID: PMC11202954 DOI: 10.3390/genes15060707] [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: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Azoospermia is a form of male infertility characterized by a complete lack of spermatozoa in the ejaculate. Sertoli cell-only syndrome (SCOS) is the most severe form of azoospermia, where no germ cells are found in the tubules. Recently, FANCM gene variants were reported as novel genetic causes of spermatogenic failure. At the same time, FANCM variants are known to be associated with cancer predisposition. We performed whole-exome sequencing on a male patient diagnosed with SCOS and a healthy father. Two compound heterozygous missense mutations in the FANCM gene were found in the patient, both being inherited from his parents. After the infertility assessment, the patient was diagnosed with diffuse astrocytoma. Immunohistochemical analyses in the testicular and tumor tissues of the patient and adequate controls showed, for the first time, not only the existence of a cytoplasmic and not nuclear pattern of FANCM in astrocytoma but also in non-mitotic neurons. In the testicular tissue of the SCOS patient, cytoplasmic anti-FANCM staining intensity appeared lower than in the control. Our case report raises a novel possibility that the infertile carriers of FANCM gene missense variants could also be prone to cancer development.
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Affiliation(s)
| | - Tihana Marić
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Lucija Žunić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Lovro Trgovec-Greif
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Filip Rokić
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Ana Fiolić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Ana Merkler Šorgić
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Davor Ježek
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Oliver Vugrek
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Antonia Jakovčević
- Department of Pathology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Maja Barbalić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
- Faculty of Science, University of Split, Rudjera Bošković 33, 21000 Split, Croatia
| | - Robert Belužić
- Laboratory for Metabolism and Aging, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Ana Katušić Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
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3
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Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Ehmke N, Seelow D, Fradin M, Kornak U, Fischer-Zirnsak B. Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy. Hum Genet 2024; 143:683-694. [PMID: 38592547 PMCID: PMC11098864 DOI: 10.1007/s00439-024-02669-y] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Generalized lipodystrophy is a feature of various hereditary disorders, often leading to a progeroid appearance. In the present study we identified a missense and a frameshift variant in a compound heterozygous state in SUPT7L in a boy with intrauterine growth retardation, generalized lipodystrophy, and additional progeroid features. SUPT7L encodes a component of the transcriptional coactivator complex STAGA. By transcriptome sequencing, we showed the predicted missense variant to cause aberrant splicing, leading to exon truncation and thereby to a complete absence of SUPT7L in dermal fibroblasts. In addition, we found altered expression of genes encoding DNA repair pathway components. This pathway was further investigated and an increased rate of DNA damage was detected in proband-derived fibroblasts and genome-edited HeLa cells. Finally, we performed transient overexpression of wildtype SUPT7L in both cellular systems, which normalizes the number of DNA damage events. Our findings suggest SUPT7L as a novel disease gene and underline the link between genome instability and progeroid phenotypes.
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Affiliation(s)
- Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Leonard A Koch
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
| | - Hristiana Lyubenova
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Oliver Küchler
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, F-35033, France
- Univercity Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, F-35000, France
| | - Erika Launay
- Service de Cytogénétique et Biologie cellulaire, Hôpital Pontchaillou - CHU Rennes, 2 rue Henri Le Guilloux - Rennes cedex 9, France, Rennes, F-35033, France
| | - Sebastian Brachs
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre Référence Déficiences Intellectuelles CRDI, Hôpital Sud - CHU Rennes, 16 boulevard de Bulgarie - BP 90347, Rennes cedex 2, Rennes, F-35203, France
- Service de Génétique, CH Saint Brieuc, St Brieuc, 22000, France
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany.
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4
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Qasim H, Khan H, Zeb H, Ahmad A, Ilyas M, Zahoor M, Umar MN, Ullah R, Ali EA. A novel variant in the FLNB gene associated with spondylocarpotarsal synostosis syndrome. J Basic Clin Physiol Pharmacol 2024; 35:181-187. [PMID: 38743867 DOI: 10.1515/jbcpp-2024-0031] [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: 03/02/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
OBJECTIVES Genetic disorders involved in skeleton system arise due to the disturbance in skeletal development, growth and homeostasis. Filamin B is an actin binding protein which is large dimeric protein which cross link actin cytoskeleton filaments into dynamic structure. A single nucleotide changes in the FLNB gene causes spondylocarpotarsal synostosis syndrome, a rare bone disorder due to which the fusion of carpels and tarsals synostosis occurred along with fused vertebrae. In the current study we investigated a family residing in north-western areas of Pakistan. METHODS The whole exome sequencing of proband was performed followed by Sanger sequencing of all family members of the subject to validate the variant segregation within the family. Bioinformatics tools were utilized to assess the pathogenicity of the variant. RESULTS Whole Exome Sequencing revealed a novel variant (NM_001457: c.209C>T and p.Pro70Leu) in the FLNB gene which was homozygous missense mutation in the FLNB gene. The variant was further validated and visualized by Sanger sequencing and protein structure studies respectively as mentioned before. CONCLUSIONS The findings have highlighted the importance of the molecular diagnosis in SCT (spondylocarpotarsal synostosis syndrome) for genetic risk counselling in consanguineous families.
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Affiliation(s)
- Hina Qasim
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar, Pakistan
| | - Hayat Khan
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar, Pakistan
| | - Humaira Zeb
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar, Pakistan
| | - Akmal Ahmad
- Centre for Human Genetics, 66934 Hazara University Mansehra , Mansehra, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar, Pakistan
| | - Muhammad Zahoor
- Department of Biochemistry, 66714 University of Malakand , Chakdara, Dir Lower, KPK, Pakistan
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, 37850 King Saud University , Riyadh, Saudi Arabia
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, 37850 College of Pharmacy King Saud University , Riyadh, Saudi Arabia
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5
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El Kassaby B, Castellanos F, Gerring M, Kunde-Ramamoorthy G, Bult CJ. MVAR: A Mouse Variation Registry. J Mol Biol 2024:168518. [PMID: 38458603 DOI: 10.1016/j.jmb.2024.168518] [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: 01/31/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
The Mouse Variation Registry (MVAR) resource is a scalable registry of mouse single nucleotide variants and small indels and variant annotation. The resource accepts data in standard Variant Call Format (VCF) and assesses the uniqueness of the submitted variants via a canonicalization process. Novel variants are assigned a unique, persistent MVAR identifier; variants that are equivalent to an existing variant in the resource are associated with the existing identifier. Annotations for variant type, molecular consequence, impact, and genomic region in the context of specific transcripts and protein sequences are generated using Ensembl's Variant Effect Predictor (VEP) and Jannovar. Access to the data and annotations in MVAR are supported via an Application Programming Interface (API) and web application. Researchers can search the resource by gene symbol, genomic region, variant (expressed in Human Genome Variation Society syntax), refSNP identifiers, or MVAR identifiers. Tabular search results can be filtered by variant annotations (variant type, molecular consequence, impact, variant region) and viewed according to variant distribution across mouse strains. The registry currently comprises more than 99 million canonical single nucleotide variants for 581 strains of mice. MVAR is accessible from https://mvar.jax.org.
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6
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Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res 2024; 34:145-159. [PMID: 38290977 PMCID: PMC10903950 DOI: 10.1101/gr.278157.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Hundreds of inbred mouse strains and intercross populations have been used to characterize the function of genetic variants that contribute to disease. Thousands of disease-relevant traits have been characterized in mice and made publicly available. New strains and populations including consomics, the collaborative cross, expanded BXD, and inbred wild-derived strains add to existing complex disease mouse models, mapping populations, and sensitized backgrounds for engineered mutations. The genome sequences of inbred strains, along with dense genotypes from others, enable integrated analysis of trait-variant associations across populations, but these analyses are hampered by the sparsity of genotypes available. Moreover, the data are not readily interoperable with other resources. To address these limitations, we created a uniformly dense variant resource by harmonizing multiple data sets. Missing genotypes were imputed using the Viterbi algorithm with a data-driven technique that incorporates local phylogenetic information, an approach that is extendable to other model organisms. The result is a web- and programmatically accessible data service called GenomeMUSter, comprising single-nucleotide variants covering 657 strains at 106.8 million segregating sites. Interoperation with phenotype databases, analytic tools, and other resources enable a wealth of applications, including multitrait, multipopulation meta-analysis. We show this in cross-species comparisons of type 2 diabetes and substance use disorder meta-analyses, leveraging mouse data to characterize the likely role of human variant effects in disease. Other applications include refinement of mapped loci and prioritization of strain backgrounds for disease modeling to further unlock extant mouse diversity for genetic and genomic studies in health and disease.
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Affiliation(s)
- Robyn L Ball
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA;
| | - Molly A Bogue
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - David G Ashbrook
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | | | | | - Alexander S Hatoum
- Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Artificial Intelligence and the Internet of Things Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Matthew J Kim
- University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hao He
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Jake Emerson
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | | | | | | | | | - Lu Lu
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - John Bluis
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Sejal Desai
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Robert W Williams
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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7
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Godfrey LK, Forster J, Liffers ST, Schröder C, Köster J, Henschel L, Ludwig KU, Lähnemann D, Trajkovic-Arsic M, Behrens D, Scarpa A, Lawlor RT, Witzke KE, Sitek B, Johnsen SA, Rahmann S, Horsthemke B, Zeschnigk M, Siveke JT. Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation. Clin Epigenetics 2024; 16:13. [PMID: 38229153 PMCID: PMC10792938 DOI: 10.1186/s13148-024-01623-z] [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: 09/19/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. It is marked by extraordinary resistance to conventional therapies including chemotherapy and radiation, as well as to essentially all targeted therapies evaluated so far. More than 90% of PDAC cases harbor an activating KRAS mutation. As the most common KRAS variants in PDAC remain undruggable so far, it seemed promising to inhibit a downstream target in the MAPK pathway such as MEK1/2, but up to now preclinical and clinical evaluation of MEK inhibitors (MEKi) failed due to inherent and acquired resistance mechanisms. To gain insights into molecular changes during the formation of resistance to oncogenic MAPK pathway inhibition, we utilized short-term passaged primary tumor cells from ten PDACs of genetically engineered mice. We followed gain and loss of resistance upon MEKi exposure and withdrawal by longitudinal integrative analysis of whole genome sequencing, whole genome bisulfite sequencing, RNA-sequencing and mass spectrometry data. RESULTS We found that resistant cell populations under increasing MEKi treatment evolved by the expansion of a single clone but were not a direct consequence of known resistance-conferring mutations. Rather, resistant cells showed adaptive DNA hypermethylation of 209 and hypomethylation of 8 genomic sites, most of which overlap with regulatory elements known to be active in murine PDAC cells. Both DNA methylation changes and MEKi resistance were transient and reversible upon drug withdrawal. Furthermore, MEKi resistance could be reversed by DNA methyltransferase inhibition with remarkable sensitivity exclusively in the resistant cells. CONCLUSION Overall, the concept of acquired therapy resistance as a result of the expansion of a single cell clone with epigenetic plasticity sheds light on genetic, epigenetic and phenotypic patterns during evolvement of treatment resistance in a tumor with high adaptive capabilities and provides potential for reversion through epigenetic targeting.
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Affiliation(s)
- Laura K Godfrey
- Bridge Institute of Experimental Tumor Therapy (BIT) and Division of Solid Tumor Translational Oncology (DKTK), West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
| | - Jan Forster
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
- Genome Informatics, Institute of Human Genetics, University Duisburg-Essen, Essen, Germany
| | - Sven-Thorsten Liffers
- Bridge Institute of Experimental Tumor Therapy (BIT) and Division of Solid Tumor Translational Oncology (DKTK), West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
| | - Christopher Schröder
- Genome Informatics, Institute of Human Genetics, University Duisburg-Essen, Essen, Germany
| | - Johannes Köster
- Bioinformatics and Computational Oncology, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn, Germany
| | - David Lähnemann
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
| | - Marija Trajkovic-Arsic
- Bridge Institute of Experimental Tumor Therapy (BIT) and Division of Solid Tumor Translational Oncology (DKTK), West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
| | - Diana Behrens
- EPO Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Germany
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Pathological Anatomy Section, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Cancer Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- ARC-Net Cancer Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Kathrin E Witzke
- Medizinisches Proteom-Center/Zentrum Für Protein-Diagnostik, Ruhr-Universität Bochum, Bochum, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center/Zentrum Für Protein-Diagnostik, Ruhr-Universität Bochum, Bochum, Germany
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Sven Rahmann
- Algorithmic Bioinformatics, Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy (BIT) and Division of Solid Tumor Translational Oncology (DKTK), West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
- German Cancer Consortium (DKTK), partner site Essen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Essen, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT) West, Campus Essen, Essen, Germany.
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8
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Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim M, He H, Emerson J, Berger AK, Walton DO, Sheppard K, Kassaby BE, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multi-trait, multi-population data integration and analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552506. [PMID: 37609331 PMCID: PMC10441370 DOI: 10.1101/2023.08.08.552506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Hundreds of inbred laboratory mouse strains and intercross populations have been used to functionalize genetic variants that contribute to disease. Thousands of disease relevant traits have been characterized in mice and made publicly available. New strains and populations including the Collaborative Cross, expanded BXD and inbred wild-derived strains add to set of complex disease mouse models, genetic mapping resources and sensitized backgrounds against which to evaluate engineered mutations. The genome sequences of many inbred strains, along with dense genotypes from others could allow integrated analysis of trait - variant associations across populations, but these analyses are not feasible due to the sparsity of genotypes available. Moreover, the data are not readily interoperable with other resources. To address these limitations, we created a uniformly dense data resource by harmonizing multiple variant datasets. Missing genotypes were imputed using the Viterbi algorithm with a data-driven technique that incorporates local phylogenetic information, an approach that is extensible to other model organism species. The result is a web- and programmatically-accessible data service called GenomeMUSter ( https://muster.jax.org ), comprising allelic data covering 657 strains at 106.8M segregating sites. Interoperation with phenotype databases, analytic tools and other resources enable a wealth of applications including multi-trait, multi-population meta-analysis. We demonstrate this in a cross-species comparison of the meta-analysis of Type 2 Diabetes and of substance use disorders, resulting in the more specific characterization of the role of human variant effects in light of mouse phenotype data. Other applications include refinement of mapped loci and prioritization of strain backgrounds for disease modeling to further unlock extant mouse diversity for genetic and genomic studies in health and disease.
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9
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Foddis M, Blumenau S, Holtgrewe M, Paquette K, Westra K, Alonso I, Macario MDC, Morgadinho AS, Velon AG, Santo G, Santana I, Mönkäre S, Kuuluvainen L, Schleutker J, Pöyhönen M, Myllykangas L, Pavlovic A, Kostic V, Dobricic V, Lohmann E, Hanagasi H, Santos M, Guven G, Bilgic B, Bras J, Beule D, Dirnagl U, Guerreiro R, Sassi C. TREX1 p.A129fs and p.Y305C variants in a large multi-ethnic cohort of CADASIL-like unrelated patients. Neurobiol Aging 2023; 123:208-215. [PMID: 36586737 DOI: 10.1016/j.neurobiolaging.2022.11.013] [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: 10/23/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) and retinal vasculopathy with cerebral leukodystrophy and systemic manifestations (RVCL-S) are the most common forms of rare monogenic early-onset cerebral small vessel disease and share clinical, and, to different extents, neuroradiological and neuropathological features. However, whether CADASIL and RVCL-S overlapping phenotype may be explained by shared genetic risk or causative factors such as TREX1 coding variants remains poorly understood. To investigate this intriguing hypothesis, we used exome sequencing to screen TREX1 protein-coding variability in a large multi-ethnic cohort of 180 early-onset independent familial and apparently sporadic CADASIL-like Caucasian patients from the USA, Portugal, Finland, Serbia and Turkey. We report 2 very rare and likely pathogenic TREX1 mutations: a loss of function mutation (p.Ala129fs) clustering in the catalytic domain, in an apparently sporadic 46-year-old patient from the USA and a missense mutation (p.Tyr305Cys) in the well conserved C-terminal region, in a 57-year-old patient with positive family history from Serbia. In concert with recent findings, our study expands the clinical spectrum of diseases associated with TREX1 mutations.
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Affiliation(s)
- Marco Foddis
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sonja Blumenau
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, BIH, Core Unit Bioinformatics and Charité - Universitätsmedizin Berlin, Berlin Germany
| | - Kimberly Paquette
- Department for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan
| | - Kaitlyn Westra
- Department for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan
| | - Isabel Alonso
- CGPP and UnIGENe, Instituto Biologia Molecular Celular, Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Maria do Carmo Macario
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Sofia Morgadinho
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Graça Velon
- Department of Neurology, Centro Hospitalar Trás-os-Montes e Alto Douro, Portugal
| | - Gustavo Santo
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Centro de Neurociências e Biologia Celular da Universidade de Coimbra, Coimbra, Portugal
| | - Isabel Santana
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Faculdade de Medicina da Universidade de Coimbra, Coimbra, Portugal; Centro de Neurociências e Biologia Celular da Universidade de Coimbra, Coimbra, Portugal
| | - Saana Mönkäre
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland; Turku University Hospital, Laboratory Division, Genomics, Department of Medical Genetics, Turku, Finland
| | - Liina Kuuluvainen
- Department of Clinical Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland; Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Johanna Schleutker
- Turku University Hospital, Laboratory Division, Genomics, Department of Medical Genetics, Turku, Finland
| | - Minna Pöyhönen
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland; Department of Clinical Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Myllykangas
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Aleksandra Pavlovic
- Clinic of Neurology, University of Belgrade, Belgrade, Serbia; Faculty for Special Education and Rehabilitation, University of Belgrade, Belgrade
| | - Vladimir Kostic
- Clinic of Neurology, University of Belgrade, Belgrade, Serbia
| | | | - Ebba Lohmann
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey; Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Hasmet Hanagasi
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mariana Santos
- UnIGENe, IBMC-Institute for Molecular and Cell Biology, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Gamze Guven
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Basar Bilgic
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Jose Bras
- Department for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan; Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Dieter Beule
- Berlin Institute of Health, BIH, Core Unit Bioinformatics and Charité - Universitätsmedizin Berlin, Berlin Germany
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Rita Guerreiro
- Department for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan; Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Celeste Sassi
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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10
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Sheth F, Shah J, Patel K, Patel D, Jain D, Sheth J, Sheth H. A novel case of two siblings harbouring homozygous variant in the NEUROG1 gene with autism as an additional phenotype: a case report. BMC Neurol 2023; 23:20. [PMID: 36647078 PMCID: PMC9841689 DOI: 10.1186/s12883-023-03065-1] [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: 09/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION NEUROG1 gene is yet to be associated with a set of human phenotypes in the OMIM database. Three cases have previously been diagnosed with cranial dysinnervation due to biallelic variants in the NEUROG1 gene. This is the fourth and a novel report of a sibling pair harboring a homozygous variant in the NEUROG1 gene with autism as an additional phenotype. A brief review of the literature in conjunction with a genotype-phenotype correlation has been described. A potential hypothesis for the presence of the autistic phenotype in the present case has also been elucidated. CASE PRESENTATION A female aged 6 years and 9 months born to endogamous and phenotypically healthy parents was diagnosed with global developmental delay, autism spectrum disorder, hearing loss, corneal opacity and no eye blinking. Her MRI of the brain revealed mild peritrigonal white matter hyperintensity, and MRI and CT scan of the temporal bones showed abnormal cranial nerves. The proband's younger sister, aged 4-years, was similarly affected. Whole exome sequencing was performed in the proband, which revealed a novel homozygous, likely pathogenic, truncating frameshift variant, c.228_231dup (p.Thr78ProfsTer122) in exon 1 of the NEUROG1 gene (ENST00000314744.4). Segregation analysis by Sanger sequencing showed the proband and her younger sister to be homozygotes and their parents to be heterozygous carriers. CONCLUSION This is the fourth report across the globe with a variant identified in the NEUROG1 gene to be associated with cranial dysinnervation phenotype. An additional phenotype of autism in two female siblings was a novel observation. We provide a hypothetical framework which could explain the pleiotropic effect of a dysfunctional NEUROG1 protein leading to autism and posit it as a candidate for diagnosis of autism spectrum disorder with congenital cranial dysinnervation disorder.
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Affiliation(s)
- Frenny Sheth
- grid.411494.d0000 0001 2154 7601FRIGE’s Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015 Satellite, Ahmedabad, India
| | - Jhanvi Shah
- grid.411494.d0000 0001 2154 7601FRIGE’s Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015 Satellite, Ahmedabad, India
| | - Ketan Patel
- Speciality Homeopathy Clinic, Ahmedabad, India
| | - Darshan Patel
- grid.448806.60000 0004 1771 0527Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, Changa, Gujarat India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Jayesh Sheth
- grid.411494.d0000 0001 2154 7601FRIGE’s Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015 Satellite, Ahmedabad, India
| | - Harsh Sheth
- grid.411494.d0000 0001 2154 7601FRIGE’s Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015 Satellite, Ahmedabad, India
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11
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Schubach M, Nazaretyan L, Kircher M. The Regulatory Mendelian Mutation score for GRCh38. Gigascience 2022; 12:giad024. [PMID: 37083939 PMCID: PMC10120424 DOI: 10.1093/gigascience/giad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/10/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Genome sequencing efforts for individuals with rare Mendelian disease have increased the research focus on the noncoding genome and the clinical need for methods that prioritize potentially disease causal noncoding variants. Some tools for assessment of variant pathogenicity as well as annotations are not available for the current human genome build (GRCh38), for which the adoption in databases, software, and pipelines was slow. RESULTS Here, we present an updated version of the Regulatory Mendelian Mutation (ReMM) score, retrained on features and variants derived from the GRCh38 genome build. Like its GRCh37 version, it achieves good performance on its highly imbalanced data. To improve accessibility and provide users with a toolbox to score their variant files and look up scores in the genome, we developed a website and API for easy score lookup. CONCLUSIONS Scores of the GRCh38 genome build are highly correlated to the prior release with a performance increase due to the better coverage of features. For prioritization of noncoding mutations in imbalanced datasets, the ReMM score performed much better than other variation scores. Prescored whole-genome files of GRCh37 and GRCh38 genome builds are cited in the article and the website; UCSC genome browser tracks, and an API are available at https://remm.bihealth.org.
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Affiliation(s)
- Max Schubach
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Lusiné Nazaretyan
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Martin Kircher
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, 23562 Lübeck, Germany
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12
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Phenotype-aware prioritisation of rare Mendelian disease variants. Trends Genet 2022; 38:1271-1283. [PMID: 35934592 PMCID: PMC9950798 DOI: 10.1016/j.tig.2022.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023]
Abstract
A molecular diagnosis from the analysis of sequencing data in rare Mendelian diseases has a huge impact on the management of patients and their families. Numerous patient phenotype-aware variant prioritisation (VP) tools have been developed to help automate this process, and shorten the diagnostic odyssey, but performance statistics on real patient data are limited. Here we identify, assess, and compare the performance of all up-to-date, freely available, and programmatically accessible tools using a whole-exome, retinal disease dataset from 134 individuals with a molecular diagnosis. All tools were able to identify around two-thirds of the genetic diagnoses as the top-ranked candidate, with LIRICAL performing best overall. Finally, we discuss the challenges to overcome most cases remaining undiagnosed after current, state-of-the-art practices.
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13
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Schipper M, Posthuma D. "Demystifying non-coding GWAS variants: an overview of computational tools and methods.". Hum Mol Genet 2022; 31:R73-R83. [PMID: 35972862 PMCID: PMC9585674 DOI: 10.1093/hmg/ddac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association studies (GWAS) have found the majority of disease-associated variants to be non-coding. Major efforts into the charting of the non-coding regulatory landscapes have allowed for the development of tools and methods which aim to aid in the identification of causal variants and their mechanism of action. In this review, we give an overview of current tools and methods for the analysis of non-coding GWAS variants in disease. We provide a workflow that allows for the accumulation of in silico evidence to generate novel hypotheses on mechanisms underlying disease and prioritize targets for follow-up study using non-coding GWAS variants. Lastly, we discuss the need for comprehensive benchmarks and novel tools for the analysis of non-coding variants.
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Affiliation(s)
- Marijn Schipper
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1105 1081HV Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1105 1081HV Amsterdam, The Netherlands
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14
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Kornak U, Saha N, Keren B, Neumann A, Taylor Tavares AL, Piard J, Kopp J, Rodrigues Alves JG, Rodríguez de Los Santos M, El Choubassi N, Ehmke N, Jäger M, Spielmann M, Pantel JT, Lejeune E, Fauler B, Mielke T, Hecht J, Meierhofer D, Strom TM, Laugel V, Brice A, Mundlos S, Bertoli-Avella A, Bauer P, Heyd F, Boute O, Dupont J, Depienne C, Van Maldergem L, Fischer-Zirnsak B. Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features. Genet Med 2022; 24:1927-1940. [PMID: 35670808 DOI: 10.1016/j.gim.2022.05.004] [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: 02/14/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE In this study we aimed to identify the molecular genetic cause of a progressive multisystem disease with prominent lipodystrophy. METHODS In total, 5 affected individuals were investigated using exome sequencing. Dermal fibroblasts were characterized using RNA sequencing, proteomics, immunoblotting, immunostaining, and electron microscopy. Subcellular localization and rescue studies were performed. RESULTS We identified a lipodystrophy phenotype with a typical facial appearance, corneal clouding, achalasia, progressive hearing loss, and variable severity. Although 3 individuals showed stunted growth, intellectual disability, and died within the first decade of life (A1, A2, and A3), 2 are adults with normal intellectual development (A4 and A5). All individuals harbored an identical homozygous nonsense variant affecting the retention and splicing complex component BUD13. The nucleotide substitution caused alternative splicing of BUD13 leading to a stable truncated protein whose expression positively correlated with disease expression and life expectancy. In dermal fibroblasts, we found elevated intron retention, a global reduction of spliceosomal proteins, and nuclei with multiple invaginations, which were more pronounced in A1, A2, and A3. Overexpression of both BUD13 isoforms normalized the nuclear morphology. CONCLUSION Our results define a hitherto unknown syndrome and show that the alternative splice product converts a loss-of-function into a hypomorphic allele, thereby probably determining the severity of the disease and the survival of affected individuals.
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Affiliation(s)
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | - Namrata Saha
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany; Max Planck International Research Network on Aging, Max Planck Society, Rostock, Germany
| | - Boris Keren
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Alexander Neumann
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Omiqa Bioinformatics, Berlin, Germany
| | - Ana Lisa Taylor Tavares
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Genomics England, London, United Kingdom
| | - Juliette Piard
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France.
| | - Johannes Kopp
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - João Guilherme Rodrigues Alves
- Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal
| | - Miguel Rodríguez de Los Santos
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany
| | - Naji El Choubassi
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, 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, Germany
| | - Marten Jäger
- 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, Germany; BIH Genomics Core Unit, Berlin Institute of Health (BIH), Berlin, Germany
| | - Malte Spielmann
- 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Jean Tori Pantel
- 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, Germany
| | - Elodie Lejeune
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jochen Hecht
- 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, Germany; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - David Meierhofer
- Mass-Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tim M Strom
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Vincent Laugel
- Service de Pédiatrie 1, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Alexis Brice
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France; Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany; Department of Medicine Clinic III, Hematology, Oncology and Palliative Medicine, Rostock University Medical Center, Rostock, Germany
| | - Florian Heyd
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Odile Boute
- Génétique Clinique, Centre Hospitalier Universitaire de Lille, Hôpital Jeanne de Flandre, Lille, France.
| | - Juliette Dupont
- Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal.
| | - Christel Depienne
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France; Center of Clinical investigation 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France
| | - 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, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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15
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Danis D, Jacobsen JOB, Balachandran P, Zhu Q, Yilmaz F, Reese J, Haimel M, Lyon GJ, Helbig I, Mungall CJ, Beck CR, Lee C, Smedley D, Robinson PN. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. Genome Med 2022; 14:44. [PMID: 35484572 PMCID: PMC9047340 DOI: 10.1186/s13073-022-01046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/12/2022] [Indexed: 01/18/2023] Open
Abstract
Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnn a .
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Affiliation(s)
- Daniel Danis
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Julius O. B. Jacobsen
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ UK
| | - Parithi Balachandran
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Qihui Zhu
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Feyza Yilmaz
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Justin Reese
- grid.184769.50000 0001 2231 4551Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Matthias Haimel
- grid.511293.d0000 0004 6104 8403Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria ,grid.416346.2St. Anna Children’s Cancer Research Institute, Vienna, Austria ,grid.418729.10000 0004 0392 6802CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria ,grid.486422.e0000000405446183Present address: Global Computational Biology and Digital Sciences, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Gholson J. Lyon
- grid.420001.70000 0000 9813 9625Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA ,grid.212340.60000000122985718Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Ingo Helbig
- grid.239552.a0000 0001 0680 8770Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
| | - Christopher J. Mungall
- grid.184769.50000 0001 2231 4551Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Christine R. Beck
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.208078.50000000419370394Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032 USA ,grid.63054.340000 0001 0860 4915Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
| | - Charles Lee
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Damian Smedley
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ UK
| | - Peter N. Robinson
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.208078.50000000419370394Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032 USA
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16
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Shah J, Patel H, Jain D, Sheth F, Sheth H. A rare case of a male child with post-zygotic de novo mosaic variant c.538C > T in MECP2 gene: a case report of Rett syndrome. BMC Neurol 2021; 21:469. [PMID: 34856927 PMCID: PMC8638266 DOI: 10.1186/s12883-021-02500-5] [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: 10/02/2021] [Accepted: 11/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is characterized by a normal perinatal period with a normal head size at birth followed by normal development for the first 6 months of life followed by gradual deceleration of head growth, loss of acquired purposeful hand skills, severe expressive and receptive language impairment, severe intellectual disability and gait and truncal apraxia/ ataxia. It is caused due to mutations in the MECP2 gene and follows an X-linked dominant mode of inheritance. It was observed exclusively in females and was believed to be lethal in males. In contrast to this belief, several males were identified with RTT upon genetic analysis, however, most males expired by the age of 2 years due to neonatal encephalopathy. The ones that survived beyond the age of 2 years, were attributed to the presence of an extra X chromosome (co-occurrence of Klinefelter and RTT) or the ones having mosaic cell lines. Only 11 males with somatic mosaicism are known till date. CASE PRESENTATION This case reports an ultra-rare case of a male affected with RTT surviving beyond the age of 2 years due to post-zygotic de novo somatic mosaicism. He was identified with a known pathogenic variant c.538C > T (p.R180*), which to the best of our knowledge is exclusively seen in females and has never been reported in a male before. CONCLUSION The present case is the first report of a mosaic male affected with RTT from India. The present report also carried out genotype-phenotype correlations across surviving mosaic males with RTT. We also postulate the effect of variant type, position along the gene and the variant allele fraction in different tissue types to be correlated with disease severity.
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Affiliation(s)
- Jhanvi Shah
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India
| | | | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India.
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India.
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Ringwald M, Richardson JE, Baldarelli RM, Blake JA, Kadin JA, Smith C, Bult CJ. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Mamm Genome 2021; 33:4-18. [PMID: 34698891 PMCID: PMC8913530 DOI: 10.1007/s00335-021-09921-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022]
Abstract
The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org .
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18
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Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res 2021; 50:D1408-D1416. [PMID: 34570217 PMCID: PMC8728305 DOI: 10.1093/nar/gkab853] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.
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Affiliation(s)
- Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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Yildirim F, Foddis M, Blumenau S, Müller S, Kajetan B, Holtgrewe M, Kola V, Beule D, Sassi C. Shared and oppositely regulated transcriptomic signatures in Huntington's disease and brain ischemia confirm known and unveil novel potential neuroprotective genes. Neurobiol Aging 2021; 104:122.e1-122.e17. [PMID: 33875290 DOI: 10.1016/j.neurobiolaging.2021.03.001] [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: 02/23/2020] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 11/20/2022]
Abstract
Huntington's disease and subcortical vascular dementia display similar dementing features, shaped by different degrees of striatal atrophy, deep white matter degeneration and tau pathology. To investigate the hypothesis that Huntington's disease transcriptomic hallmarks may provide a window into potential protective genes upregulated during brain acute and subacute ischemia, we compared RNA sequencing signatures in the most affected brain areas of 2 widely used experimental mouse models: Huntington's disease, (R6/2, striatum and cortex and Q175, hippocampus) and brain ischemia-subcortical vascular dementia (BCCAS, striatum, cortex and hippocampus). We identified a cluster of 55 shared genes significantly differentially regulated in both models and we screened these in 2 different mouse models of Alzheimer's disease, and 96 early-onset familial and apparently sporadic small vessel ischemic disease patients. Our data support the prevalent role of transcriptional regulation upon genetic coding variability of known neuroprotective genes (Egr2, Fos, Ptgs2, Itga5, Cdkn1a, Gsn, Npas4, Btg2, Cebpb) and provide a list of potential additional ones likely implicated in different dementing disorders and worth further investigation.
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Affiliation(s)
- Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Foddis
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sonja Blumenau
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susanne Müller
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Bentele Kajetan
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Vasilis Kola
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, BIH, Core Unit Bioinformatics, Berlin, Germany
| | - Celeste Sassi
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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20
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PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice. Sci Rep 2021; 11:6072. [PMID: 33727568 PMCID: PMC7966789 DOI: 10.1038/s41598-021-84919-x] [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: 04/10/2020] [Accepted: 02/04/2021] [Indexed: 11/29/2022] Open
Abstract
Recently, several genome-wide association studies identified PHACTR1 as key locus for five diverse vascular disorders: coronary artery disease, migraine, fibromuscular dysplasia, cervical artery dissection and hypertension. Although these represent significant risk factors or comorbidities for ischemic stroke, PHACTR1 role in brain small vessel ischemic disease and ischemic stroke most important survival mechanism, such as the recruitment of brain collateral arteries like posterior communicating arteries (PcomAs), remains unknown. Therefore, we applied exome and genome sequencing in a multi-ethnic cohort of 180 early-onset independent familial and apparently sporadic brain small vessel ischemic disease and CADASIL-like Caucasian patients from US, Portugal, Finland, Serbia and Turkey and in 2 C57BL/6J stroke mouse models (bilateral common carotid artery stenosis [BCCAS] and middle cerebral artery occlusion [MCAO]), characterized by different degrees of PcomAs patency. We report 3 very rare coding variants in the small vessel ischemic disease-CADASIL-like cohort (p.Glu198Gln, p.Arg204Gly, p.Val251Leu) and a stop-gain mutation (p.Gln273*) in one MCAO mouse. These coding variants do not cluster in PHACTR1 known pathogenic domains and are not likely to play a critical role in small vessel ischemic disease or brain collateral circulation. We also exclude the possibility that copy number variants (CNVs) or a variant enrichment in Phactr1 may be associated with PcomA recruitment in BCCAS mice or linked to diverse vascular traits (cerebral blood flow pre-surgery, PcomA size, leptomeningeal microcollateral length and junction density during brain hypoperfusion) in C57BL/6J mice, respectively. Genetic variability in PHACTR1 is not likely to be a common susceptibility factor influencing small vessel ischemic disease in patients and PcomA recruitment in C57BL/6J mice. Nonetheless, rare variants in PHACTR1 RPEL domains may influence the stroke outcome and are worth investigating in a larger cohort of small vessel ischemic disease patients, different ischemic stroke subtypes and with functional studies.
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21
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Huang D, Yi X, Zhou Y, Yao H, Xu H, Wang J, Zhang S, Nong W, Wang P, Shi L, Xuan C, Li M, Wang J, Li W, Kwan HS, Sham PC, Wang K, Li MJ. Ultrafast and scalable variant annotation and prioritization with big functional genomics data. Genome Res 2020; 30:1789-1801. [PMID: 33060171 PMCID: PMC7706736 DOI: 10.1101/gr.267997.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers.
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Affiliation(s)
- Dandan Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Hang Xu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Panwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Miaoxin Li
- Center for Genome Research, Center for Precision Medicine, Zhongshan School of Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Weidong Li
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre of Genomics Sciences, Departments of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Mulin Jun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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22
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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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23
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Charid I, Kessler M, Darb-Esfahani S, Zemojtel T, Abobaker S, Tyuarets S, Schrauwen S, Atmani-Kilani D, Benaida-Debbache N, Schäfer R, Castillo-Tong DC, Atmani D, Cherbal F, Amant F, Sehouli J, Kulbe H, Braicu EI. Pretreatment with methanolic extract of Pistacia lentiscus L. increases sensitivity to DNA damaging drugs in primary high-grade serous ovarian cancer cells. Eur J Integr Med 2020. [DOI: 10.1016/j.eujim.2020.101163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Messerschmidt C, Obermayer B, Klinghammer K, Ochsenreither S, Treue D, Stenzinger A, Glimm H, Fröhling S, Kindler T, Brandts CH, Schulze-Osthoff K, Weichert W, Tinhofer I, Klauschen F, Keilholz U, Beule D, Rieke DT. Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC. Int J Cancer 2020; 147:2293-2302. [PMID: 32468570 DOI: 10.1002/ijc.33123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibition leads to response in some patients with head and neck squamous cell carcinoma (HNSCC). Robust biomarkers are lacking to date. We analyzed viral status, gene expression signatures, mutational load and mutational signatures in whole exome and RNA-sequencing data of the HNSCC TCGA dataset (n = 496) and a validation set (DKTK MASTER cohort, n = 10). Public single-cell gene expression data from 17 HPV-negative HNSCC were separately reanalyzed. APOBEC3-associated TCW motif mutations but not total single nucleotide variant burden were significantly associated with inflammation. This association was restricted to HPV-negative HNSCC samples. An APOBEC-enriched, HPV-negative subgroup was identified, that showed higher T-cell inflammation and immune checkpoint expression, as well as expression of APOBEC3 genes. Mutations in immune-evasion pathways were also enriched in these tumors. Analysis of single-cell sequencing data identified expression of APOBEC3B and 3C genes in malignant cells. We identified an APOBEC-enriched subgroup of HPV-negative HNSCC with a distinct immunogenic phenotype, potentially mediating response to immunotherapy.
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Affiliation(s)
- Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany
| | - Sebastian Ochsenreither
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Denise Treue
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany.,University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kindler
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Hematology, Medical Oncology & Pneumology, University Medical Center, Mainz, Germany.,University Cancer Center Mainz (UCT), Johannes Gutenberg-University, Mainz, Germany
| | - Christian H Brandts
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,University Cancer Center Frankfurt (UCT), Goethe University Frankfurt, Frankfurt, Germany.,Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Klaus Schulze-Osthoff
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Interfaculty Institute of Biochemistry, Tübingen University, Tübingen, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Damian T Rieke
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
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25
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Petrini A, Mesiti M, Schubach M, Frasca M, Danis D, Re M, Grossi G, Cappelletti L, Castrignanò T, Robinson PN, Valentini G. parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants. Gigascience 2020; 9:giaa052. [PMID: 32444882 PMCID: PMC7244787 DOI: 10.1093/gigascience/giaa052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/31/2019] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data. RESULTS To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version. CONCLUSIONS parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.
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Affiliation(s)
- Alessandro Petrini
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Marco Mesiti
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Max Schubach
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Marco Frasca
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington (CT) - 06032, United States of America
| | - Matteo Re
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Giuliano Grossi
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Luca Cappelletti
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
| | - Tiziana Castrignanò
- CINECA, SCAI SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy
- University of Tuscia, Department of Ecological and Biological Sciences (DEB), Largo dell'Università snc, 01100 Viterbo, Italy
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington (CT) - 06032, United States of America
| | - Giorgio Valentini
- Università degli Studi di Milano, AnacletoLab - Dipartimento di Informatica, via Giovanni Celoria 18, 20135 Milano, Italy
- CINI National Laboratory in Artificial Intelligence and Intelligent Systems - AIIS, Università di Roma, Via Ariosto 25, 00185 Roma, Italy
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26
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Investigating APOE, APP-Aβ metabolism genes and Alzheimer's disease GWAS hits in brain small vessel ischemic disease. Sci Rep 2020; 10:7103. [PMID: 32345996 PMCID: PMC7188838 DOI: 10.1038/s41598-020-63183-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/13/2020] [Indexed: 12/24/2022] Open
Abstract
Alzheimer’s disease and small vessel ischemic disease frequently co-exist in the aging brain. However, pathogenic links between these 2 disorders are yet to be identified. Therefore we used Taqman genotyping, exome and RNA sequencing to investigate Alzheimer’s disease known pathogenic variants and pathways: APOE ε4 allele, APP-Aβ metabolism and late-onset Alzheimer’s disease main genome-wide association loci (APOE, BIN1, CD33, MS4A6A, CD2AP, PICALM, CLU, CR1, EPHA1, ABCA7) in 96 early-onset small vessel ischemic disease Caucasian patients and 368 elderly neuropathologically proven controls (HEX database) and in a mouse model of cerebral hypoperfusion. Only a minority of patients (29%) carried APOE ε4 allele. We did not detect any pathogenic mutation in APP, PSEN1 and PSEN2 and report a burden of truncating mutations in APP-Aß degradation genes. The single-variant association test identified 3 common variants with a likely protective effect on small vessel ischemic disease (0.54>OR > 0.32, adj. p-value <0.05) (EPHA1 p.M900V and p.V160A and CD33 p.A14V). Moreover, 5/17 APP-Aß catabolism genes were significantly upregulated (LogFC > 1, adj. p-val<0.05) together with Apoe, Ms4a cluster and Cd33 during brain hypoperfusion and their overexpression correlated with the ischemic lesion size. Finally, the detection of Aβ oligomers in the hypoperfused hippocampus supported the link between brain ischemia and Alzheimer’s disease pathology.
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27
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Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M, Webster AR, Moore AT, Robinson PN, Jacobsen JO, Smedley D. An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. Genes (Basel) 2020; 11:E460. [PMID: 32340307 PMCID: PMC7230372 DOI: 10.3390/genes11040460] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients' sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein-protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients' HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.
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Affiliation(s)
- Valentina Cipriani
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- UCL Genetics Institute, University College London, London WC1E 6AA, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital NHS Trust, London WC1N 3BH, UK
| | | | - Eva Lenassi
- Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK; (P.I.S.); (E.L.)
| | - Penpitcha Thawong
- Department of Medical Sciences, Medical Genetics Section, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Andrew R. Webster
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Anthony T. Moore
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Ophthalmology Department, UCSF School of Medicine, San Francisco, CA 94143-0644, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
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28
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Ehmke N, Cusmano-Ozog K, Koenig R, Holtgrewe M, Nur B, Mihci E, Babcock H, Gonzaga-Jauregui C, Overton JD, Xiao J, Martinez AF, Muenke M, Balzer A, Jochim J, El Choubassi N, Fischer-Zirnsak B, Huber C, Kornak U, Elsea SH, Cormier-Daire V, Ferreira CR. Biallelic variants in KYNU cause a multisystemic syndrome with hand hyperphalangism. Bone 2020; 133:115219. [PMID: 31923704 PMCID: PMC10521254 DOI: 10.1016/j.bone.2019.115219] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/25/2019] [Accepted: 12/29/2019] [Indexed: 01/17/2023]
Abstract
Catel-Manzke syndrome is characterized by the combination of Pierre Robin sequence and radial deviation, shortening as well as clinodactyly of the index fingers, due to an accessory ossification center. Mutations in TGDS have been identified as one cause of Catel-Manzke syndrome, but cannot be found as causative in every patient with the clinical diagnosis. We performed a chromosome microarray and/or exome sequencing in three patients with hand hyperphalangism, heart defect, short stature, and mild to severe developmental delay, all of whom were initially given a clinical diagnosis of Catel-Manzke syndrome. In one patient, we detected a large deletion of exons 1-8 and the missense variant c.1282C > T (p.Arg428Trp) in KYNU (NM_003937.2), whereas homozygous missense variants in KYNU were found in the other two patients (c.989G > A (p.Arg330Gln) and c.326G > C (p.Trp109Ser)). Plasma and urine metabolomic analysis of two patients indicated a block along the tryptophan catabolic pathway and urine organic acid analysis showed excretion of xanthurenic acid. Biallelic loss-of-function mutations in KYNU were recently described as a cause of NAD deficiency with vertebral, cardiac, renal and limb defects; however, no hand hyperphalangism was described in those patients, and Catel-Manzke syndrome was not discussed as a differential diagnosis. In conclusion, we present unrelated patients identified with biallelic variants in KYNU leading to kynureninase deficiency and xanthurenic aciduria as a very likely cause of their hyperphalangism, heart defect, short stature, and developmental delay. We suggest performance of urine organic acid analysis in patients with suspected Catel-Manzke syndrome, particularly in those with cardiac or vertebral defects or without mutations in TGDS.
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Affiliation(s)
- Nadja Ehmke
- Charité - Universitätsmedizin Berlin, Institute of Medical Genetics and Human Genetics, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestr. 63-73, 14195 Berlin, Germany.
| | - Kristina Cusmano-Ozog
- Biochemical Genetics and Metabolism Laboratory, Children's National Hospital, Washington, DC 20010, USA
| | - Rainer Koenig
- Department of Human Genetics, University of Frankfurt, 60590 Frankfurt, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; Charité - Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Banu Nur
- Department of Pediatric Genetics, Akdeniz University Medical School, 07059 Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University Medical School, 07059 Antalya, Turkey
| | - Holly Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | | | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10599, USA
| | - Jing Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ariel F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Judith Jochim
- Sana Klinikum Offenbach GmbH, Starkenburgring 66, 63069 Offenbach am Main, Germany
| | - Naji El Choubassi
- Charité - Universitätsmedizin Berlin, Institute of Medical Genetics and Human Genetics, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Föhrerstr. 15, 13353 Berlin, Germany
| | - Björn Fischer-Zirnsak
- Charité - Universitätsmedizin Berlin, Institute of Medical Genetics and Human Genetics, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Föhrerstr. 15, 13353 Berlin, Germany
| | - Céline Huber
- Department of Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker Enfants Malades, 75015 Paris, France
| | - Uwe Kornak
- Charité - Universitätsmedizin Berlin, Institute of Medical Genetics and Human Genetics, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Föhrerstr. 15, 13353 Berlin, Germany
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valérie Cormier-Daire
- Department of Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker Enfants Malades, 75015 Paris, France
| | - Carlos R Ferreira
- Department of Pediatric Genetics, Akdeniz University Medical School, 07059 Antalya, Turkey; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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Seidel E, Walenda G, Messerschmidt C, Obermayer B, Peitzsch M, Wallace P, Bahethi R, Yoo T, Choi M, Schrade P, Bachmann S, Liebisch G, Eisenhofer G, Beule D, Scholl UI. Generation and characterization of a mitotane-resistant adrenocortical cell line. Endocr Connect 2020; 9:122-134. [PMID: 31910152 PMCID: PMC6993260 DOI: 10.1530/ec-19-0510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/06/2020] [Indexed: 12/11/2022]
Abstract
Mitotane is the only drug approved for the therapy of adrenocortical carcinoma (ACC). Its clinical use is limited by the occurrence of relapse during therapy. To investigate the underlying mechanisms in vitro, we here generated mitotane-resistant cell lines. After long-term pulsed treatment of HAC-15 human adrenocortical carcinoma cells with 70 µM mitotane, we isolated monoclonal cell populations of treated cells and controls and assessed their respective mitotane sensitivities by MTT assay. We performed exome sequencing and electron microscopy, conducted gene expression microarray analysis and determined intracellular lipid concentrations in the presence and absence of mitotane. Clonal cell lines established after pulsed treatment were resistant to mitotane (IC50 of 102.2 ± 7.3 µM (n = 12) vs 39.4 ± 6.2 µM (n = 6) in controls (biological replicates, mean ± s.d., P = 0.0001)). Unlike nonresistant clones, resistant clones maintained normal mitochondrial and nucleolar morphology during mitotane treatment. Resistant clones largely shared structural and single nucleotide variants, suggesting a common cell of origin. Resistance depended, in part, on extracellular lipoproteins and was associated with alterations in intracellular lipid homeostasis, including levels of free cholesterol, as well as decreased steroid production. By gene expression analysis, resistant cells showed profound alterations in pathways including steroid metabolism and transport, apoptosis, cell growth and Wnt signaling. These studies establish an in vitro model of mitotane resistance in ACC and point to underlying molecular mechanisms. They may enable future studies to overcome resistance in vitro and improve ACC treatment in vivo.
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Affiliation(s)
- Eric Seidel
- 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, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Department of Nephrology, School of Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gudrun Walenda
- Department of Nephrology, School of Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Clemens Messerschmidt
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Benedikt Obermayer
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Paal Wallace
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Rohini Bahethi
- Department of Nephrology, School of Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Petra Schrade
- Charité – Universitaetsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Vegetative Anatomie, Berlin, Germany
| | - Sebastian Bachmann
- Charité – Universitaetsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Vegetative Anatomie, Berlin, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ute I Scholl
- 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, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Department of Nephrology, School of Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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30
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Holt JM, Wilk B, Birch CL, Brown DM, Gajapathy M, Moss AC, Sosonkina N, Wilk MA, Anderson JA, Harris JM, Kelly JM, Shaterferdosian F, Uno-Antonison AE, Weborg A, Worthey EA. VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC Bioinformatics 2019; 20:496. [PMID: 31615419 PMCID: PMC6792253 DOI: 10.1186/s12859-019-3026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance. METHODS We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network. RESULTS We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20. CONCLUSIONS We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.
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Affiliation(s)
- James M. Holt
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Brandon Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Camille L. Birch
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Donna M. Brown
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Manavalan Gajapathy
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Alexander C. Moss
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Nadiya Sosonkina
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
- University of Alabama at Birmingham, Department of Genetics, 720 20th Street South, Birmingham, 35294 USA
| | - Melissa A. Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Julie A. Anderson
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jeremy M. Harris
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jacob M. Kelly
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Fariba Shaterferdosian
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Angelina E. Uno-Antonison
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Arthur Weborg
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Elizabeth A. Worthey
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
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Thole TM, Toedling J, Sprüssel A, Pfeil S, Savelyeva L, Capper D, Messerschmidt C, Beule D, Groeneveld-Krentz S, Eckert C, Gambara G, Henssen AG, Finkler S, Schulte JH, Sieber A, Bluethgen N, Regenbrecht CRA, Künkele A, Lodrini M, Eggert A, Deubzer HE. Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model. Int J Cancer 2019; 146:1031-1041. [PMID: 31304977 DOI: 10.1002/ijc.32572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023]
Abstract
Accurate modeling of intratumor heterogeneity presents a bottleneck against drug testing. Flexibility in a preclinical platform is also desirable to support assessment of different endpoints. We established the model system, OHC-NB1, from a bone marrow metastasis from a patient diagnosed with MYCN-amplified neuroblastoma and performed whole-exome sequencing on the source metastasis and the different models and passages during model development (monolayer cell line, 3D spheroid culture and subcutaneous xenograft tumors propagated in mice). OHC-NB1 harbors a MYCN amplification in double minutes, 1p deletion, 17q gain and diploid karyotype, which persisted in all models. A total of 80-540 single-nucleotide variants (SNVs) was detected in each sample, and comparisons between the source metastasis and models identified 34 of 80 somatic SNVs to be propagated in the models. Clonal reconstruction using the combined copy number and SNV data revealed marked clonal heterogeneity in the originating metastasis, with four clones being reflected in the model systems. The set of OHC-NB1 models represents 43% of somatic SNVs and 23% of the cellularity in the originating metastasis with varying clonal compositions, indicating that heterogeneity is partially preserved in our model system.
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Affiliation(s)
- Theresa M Thole
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Joern Toedling
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Sprüssel
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Pfeil
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Savelyeva
- Research Group Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | | | - Cornelia Eckert
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Guido Gambara
- CELLPhenomics GmbH, Berlin, Germany.,Charité Comprehensive Cancer Center (CCCC), Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Sabine Finkler
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Anja Sieber
- Computational Modelling in Medicine, Charité - Universitätsmedizin Berlin, Institute for Pathology, Berlin, Germany.,IRI Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Nils Bluethgen
- Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany.,Computational Modelling in Medicine, Charité - Universitätsmedizin Berlin, Institute for Pathology, Berlin, Germany.,IRI Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Christian R A Regenbrecht
- CELLPhenomics GmbH, Berlin, Germany.,Department for Pathology, Medical Faculty, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - Annette Künkele
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Marco Lodrini
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany.,Neuroblastoma Research Group, Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
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32
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Jones RM, Melton PE, Pinese M, Rea AJ, Ingley E, Ballinger ML, Wood DJ, Thomas DM, Moses EK. Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts. BMC MEDICAL GENETICS 2019; 20:69. [PMID: 31053105 PMCID: PMC6499942 DOI: 10.1186/s12881-019-0808-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/16/2019] [Indexed: 12/26/2022]
Abstract
Background Although familial clustering of cancers is relatively common, only a small proportion of familial cancer risk can be explained by known cancer predisposition genes. Methods In this study we employed a two-stage approach to identify candidate sarcoma risk genes. First, we conducted whole exome sequencing in three multigenerational cancer families ascertained through a sarcoma proband (n = 19) in order to prioritize candidate genes for validation in an independent case-control cohort of sarcoma patients using family-based association and segregation analysis. The second stage employed a burden analysis of rare variants within prioritized candidate genes identified from stage one in 560 sarcoma cases and 1144 healthy ageing controls, for which whole genome sequence was available. Results Variants from eight genes were identified in stage one. Following gene-based burden testing and after correction for multiple testing, two of these genes, ABCB5 and C16orf96, were determined to show statistically significant association with cancer. The ABCB5 gene was found to have a higher burden of putative regulatory variants (OR = 4.9, p-value = 0.007, q-value = 0.04) based on allele counts in sarcoma cases compared to controls. C16orf96, was found to have a significantly lower burden (OR = 0.58, p-value = 0.0004, q-value = 0.003) of regulatory variants in controls compared to sarcoma cases. Conclusions Based on these genetic association data we propose that ABCB5 and C16orf96 are novel candidate risk genes for sarcoma. Although neither of these two genes have been previously associated with sarcoma, ABCB5 has been shown to share clinical drug resistance associations with melanoma and leukaemia and C16orf96 shares regulatory elements with genes that are involved with TNF-alpha mediated apoptosis in a p53/TP53-dependent manner. Future genetic studies in other family and population cohorts will be required for further validation of these novel findings. Electronic supplementary material The online version of this article (10.1186/s12881-019-0808-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel M Jones
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia.,Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia
| | - Phillip E Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia.,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Western Australia
| | - Mark Pinese
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Alexander J Rea
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia
| | - Evan Ingley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.,Harry Perkins Institute of Medical Research, Murdoch, Western Australia.,The Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - David J Wood
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia
| | - David M Thomas
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eric K Moses
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia. .,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Western Australia. .,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia.
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33
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Bramswig NC, Bertoli-Avella AM, Albrecht B, Al Aqeel AI, Alhashem A, Al-Sannaa N, Bah M, Bröhl K, Depienne C, Dorison N, Doummar D, Ehmke N, Elbendary HM, Gorokhova S, Héron D, Horn D, James K, Keren B, Kuechler A, Ismail S, Issa MY, Marey I, Mayer M, McEvoy-Venneri J, Megarbane A, Mignot C, Mohamed S, Nava C, Philip N, Ravix C, Rolfs A, Sadek AA, Segebrecht L, Stanley V, Trautman C, Valence S, Villard L, Wieland T, Engels H, Strom TM, Zaki MS, Gleeson JG, Lüdecke HJ, Bauer P, Wieczorek D. Genetic variants in components of the NALCN-UNC80-UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies). Hum Genet 2018; 137:753-768. [PMID: 30167850 PMCID: PMC6671679 DOI: 10.1007/s00439-018-1929-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/30/2022]
Abstract
NALCN is a conserved cation channel, which conducts a permanent sodium leak current and regulates resting membrane potential and neuronal excitability. It is part of a large ion channel complex, the "NALCN channelosome", consisting of multiple proteins including UNC80 and UNC79. The predominant neuronal expression pattern and its function suggest an important role in neuronal function and disease. So far, biallelic NALCN and UNC80 variants have been described in a small number of individuals leading to infantile hypotonia, psychomotor retardation, and characteristic facies 1 (IHPRF1, OMIM 615419) and 2 (IHPRF2, OMIM 616801), respectively. Heterozygous de novo NALCN missense variants in the S5/S6 pore-forming segments lead to congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD, OMIM 616266) with some clinical overlap. In this study, we present detailed clinical information of 16 novel individuals with biallelic NALCN variants, 1 individual with a heterozygous de novo NALCN missense variant and an interesting clinical phenotype without contractures, and 12 individuals with biallelic UNC80 variants. We report for the first time a missense NALCN variant located in the predicted S6 pore-forming unit inherited in an autosomal-recessive manner leading to mild IHPRF1. We show evidence of clinical variability, especially among IHPRF1-affected individuals, and discuss differences between the IHPRF1- and IHPRF2 phenotypes. In summary, we provide a comprehensive overview of IHPRF1 and IHPRF2 phenotypes based on the largest cohort of individuals reported so far and provide additional insights into the clinical phenotypes of these neurodevelopmental diseases to help improve counseling of affected families.
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Affiliation(s)
- Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | | | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Aida I Al Aqeel
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- American University of Beirut, Beirut, Lebanon
- Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Nouriya Al-Sannaa
- John Hopkins Aramco Health Care, Pediatric Services, Dhahran, Saudi Arabia
| | - Maissa Bah
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Katharina Bröhl
- Internal Medicine Department, Waldkrankenhaus Evangelical Hospital, Berlin, Germany
| | - Christel Depienne
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, 75013, Paris, France
| | - Nathalie Dorison
- Service de Neurochirurgie Pédiatrique, Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Diane Doummar
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Nadja Ehmke
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Hasnaa M Elbendary
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Svetlana Gorokhova
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Delphine Héron
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Denise Horn
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kiely James
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Boris Keren
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Samira Ismail
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Isabelle Marey
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Michèle Mayer
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Jennifer McEvoy-Venneri
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Andre Megarbane
- CEMEDIPP-Centre Medico Psychopedagogique, Beirut, Lebanon
- Institut Jerome Lejeune, Paris, France
| | - Cyril Mignot
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Sarar Mohamed
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Prince Abdullah bin Khaled Coeliac Disease Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Caroline Nava
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, 75013, Paris, France
| | - Nicole Philip
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Cecile Ravix
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Arndt Rolfs
- CENTOGENE AG, The Rare Disease Company, Rostock, Germany
- Albrecht Kossel Institute, University of Rostock, Rostock, Germany
| | - Abdelrahim Abdrabou Sadek
- Pediatric Neurology Unit, Department of Pediatrics, Faculty of Medicine, Sohag University, Sohâg, Egypt
| | - Lara Segebrecht
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Camille Trautman
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Stephanie Valence
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Laurent Villard
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Peter Bauer
- CENTOGENE AG, The Rare Disease Company, Rostock, Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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Hematopoietic lineage distribution and evolutionary dynamics of clonal hematopoiesis. Leukemia 2018; 32:1908-1919. [PMID: 29491455 DOI: 10.1038/s41375-018-0047-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/27/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) occurs in an age-related manner and associates with an increased risk of hematologic cancer, atherosclerotic disease, and shorter overall survival. Little is known about the cell of origin, repartition patterns of clonal mutations within the hematopoietic differentiation tree, and its dynamics under evolutionary pressure. Using targeted sequencing, CHIP was identified in 121 out of 437 elderly individuals (27.7%). Variant allele frequencies (VAFs) of 91 mutations were studied in six peripheral blood cell fractions. VAFs were significantly higher in monocytes, granulocytes, and NK-cells compared to B- or T cells. In all cases with available bone marrow material, mutations could be identified in Lin-CD34+CD38- HSCs with subsequent expansion to myeloid primed progenitors. In 22 patients with solid cancer receiving (radio-)chemotherapy, longitudinal study of 32 mutations at 121 time points identified relative VAF changes of at least 50% in 13/32 mutations. VAFs of DNMT3A, were stable in 12/13 cases (P < .001). Cancer patients with a clonal mutation other than DNMT3A required more often red blood cell transfusions and dose reductions. Our results provide novel insights into cellular distribution of clonal mutations, their dynamics under chemotherapy, and advocate for systematic analyses for CHIP in cancer patients.
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35
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Ehmke N, Graul-Neumann L, Smorag L, Koenig R, Segebrecht L, Magoulas P, Scaglia F, Kilic E, Hennig AF, Adolphs N, Saha N, Fauler B, Kalscheuer VM, Hennig F, Altmüller J, Netzer C, Thiele H, Nürnberg P, Yigit G, Jäger M, Hecht J, Krüger U, Mielke T, Krawitz PM, Horn D, Schuelke M, Mundlos S, Bacino CA, Bonnen PE, Wollnik B, Fischer-Zirnsak B, Kornak U. De Novo Mutations in SLC25A24 Cause a Craniosynostosis Syndrome with Hypertrichosis, Progeroid Appearance, and Mitochondrial Dysfunction. Am J Hum Genet 2017; 101:833-843. [PMID: 29100093 DOI: 10.1016/j.ajhg.2017.09.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/19/2017] [Indexed: 12/28/2022] Open
Abstract
Gorlin-Chaudhry-Moss syndrome (GCMS) is a dysmorphic syndrome characterized by coronal craniosynostosis and severe midface hypoplasia, body and facial hypertrichosis, microphthalmia, short stature, and short distal phalanges. Variable lipoatrophy and cutis laxa are the basis for a progeroid appearance. Using exome and genome sequencing, we identified the recurrent de novo mutations c.650G>A (p.Arg217His) and c.649C>T (p.Arg217Cys) in SLC25A24 in five unrelated girls diagnosed with GCMS. Two of the girls had pronounced neonatal progeroid features and were initially diagnosed with Wiedemann-Rautenstrauch syndrome. SLC25A24 encodes a mitochondrial inner membrane ATP-Mg/Pi carrier. In fibroblasts from affected individuals, the mutated SLC25A24 showed normal stability. In contrast to control cells, the probands' cells showed mitochondrial swelling, which was exacerbated upon treatment with hydrogen peroxide (H2O2). The same effect was observed after overexpression of the mutant cDNA. Under normal culture conditions, the mitochondrial membrane potential of the probands' fibroblasts was intact, whereas ATP content in the mitochondrial matrix was lower than that in control cells. However, upon H2O2 exposure, the membrane potential was significantly elevated in cells harboring the mutated SLC25A24. No reduction of mitochondrial DNA copy number was observed. These findings demonstrate that mitochondrial dysfunction with increased sensitivity to oxidative stress is due to the SLC25A24 mutations. Our results suggest that the SLC25A24 mutations induce a gain of pathological function and link mitochondrial ATP-Mg/Pi transport to the development of skeletal and connective tissue.
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36
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Pal LR, Kundu K, Yin Y, Moult J. CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants. Hum Mutat 2017; 38:1169-1181. [PMID: 28512736 PMCID: PMC5577808 DOI: 10.1002/humu.23257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/21/2022]
Abstract
Compared with earlier more restricted sequencing technologies, identification of rare disease variants using whole-genome sequence has the possibility of finding all causative variants, but issues of data quality and an overwhelming level of background variants complicate the analysis. The CAGI4 SickKids clinical genome challenge provided an opportunity to assess the landscape of variants found in a difficult set of 25 unsolved rare disease cases. To address the challenge, we developed a three-stage pipeline, first carefully analyzing data quality, then classifying high-quality gene-specific variants into seven categories, and finally examining each candidate variant for compatibility with the often complex phenotypes of these patients for final prioritization. Variants consistent with the phenotypes were found in 24 out of the 25 cases, and in a number of these, there are prioritized variants in multiple genes. Data quality analysis suggests that some of the selected variants are likely incorrect calls, complicating interpretation. The data providers followed up on three suggested variants with Sanger sequencing, and in one case, a prioritized variant was confirmed as likely causative by the referring physician, providing a diagnosis in a previously intractable case.
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Affiliation(s)
- Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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Trubicka J, Żemojtel T, Hecht J, Falana K, Piekutowska- Abramczuk D, Płoski R, Perek-Polnik M, Drogosiewicz M, Grajkowska W, Ciara E, Moszczyńska E, Dembowska-Bagińska B, Perek D, Chrzanowska KH, Krajewska-Walasek M, Łastowska M. The germline variants in DNA repair genes in pediatric medulloblastoma: a challenge for current therapeutic strategies. BMC Cancer 2017; 17:239. [PMID: 28376765 PMCID: PMC5379555 DOI: 10.1186/s12885-017-3211-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/22/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The defects in DNA repair genes are potentially linked to development and response to therapy in medulloblastoma. Therefore the purpose of this study was to establish the spectrum and frequency of germline variants in selected DNA repair genes and their impact on response to chemotherapy in medulloblastoma patients. METHODS The following genes were investigated in 102 paediatric patients: MSH2 and RAD50 using targeted gene panel sequencing and NBN variants (p.I171V and p.K219fs*19) by Sanger sequencing. In three patients with presence of rare life-threatening adverse events (AE) and no detected variants in the analyzed genes, whole exome sequencing was performed. Based on combination of molecular and immunohistochemical evaluations tumors were divided into molecular subgroups. Presence of variants was tested for potential association with the occurrence of rare life-threatening AE and other clinical features. RESULTS We have identified altogether six new potentially pathogenic variants in MSH2 (p.A733T and p.V606I), RAD50 (p.R1093*), FANCM (p.L694*), ERCC2 (p.R695C) and EXO1 (p.V738L), in addition to two known NBN variants. Five out of twelve patients with defects in either of MSH2, RAD50 and NBN genes suffered from rare life-threatening AE, more frequently than in control group (p = 0.0005). When all detected variants were taken into account, the majority of patients (8 out of 15) suffered from life-threatening toxicity during chemotherapy. CONCLUSION Our results, based on the largest systematic study performed in a clinical setting, provide preliminary evidence for a link between defects in DNA repair genes and treatment related toxicity in children with medulloblastoma. The data suggest that patients with DNA repair gene variants could need special vigilance during and after courses of chemotherapy.
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Affiliation(s)
- Joanna Trubicka
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
- Department of Pathology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Tomasz Żemojtel
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Katarzyna Falana
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Dorota Piekutowska- Abramczuk
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Marta Perek-Polnik
- Department of Oncology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Monika Drogosiewicz
- Department of Oncology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
- Department of Experimental and Clinical Pathology, Mossakowski Medical Research Centre Polish Academy of Sciences, A. Pawińskiego 5, 02-106 Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Elżbieta Moszczyńska
- Department of Endocrinology and Diabetology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Bożenna Dembowska-Bagińska
- Department of Oncology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Danuta Perek
- Department of Oncology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Krystyna H. Chrzanowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Małgorzata Krajewska-Walasek
- Department of Medical Genetics, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Maria Łastowska
- Department of Pathology, The Children’s Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
- Department of Experimental and Clinical Pathology, Mossakowski Medical Research Centre Polish Academy of Sciences, A. Pawińskiego 5, 02-106 Warsaw, Poland
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Köhler S, Robinson PN. [Diagnostics in human genetics : Integration of phenotypic and genomic data]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2017; 60:542-549. [PMID: 28293716 DOI: 10.1007/s00103-017-2538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The development of reliable methods for annotation of clinical phenotypes and algorithms to calculate similarity values for clinical phenotype profiles will be a major challenge for genomic personalized medicine, since combined analysis of phenotypic features and genetic variants can increase diagnostic yield, especially with exome or genome sequencing. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for capturing phenotypic abnormalities in human disease in a precise and comprehensive fashion. The HPO not only enables reliable integration of disease-relevant information from numerous databases, but it also allows for similarity between patients or between patients and disease descriptions to be calculated algorithmically. The HPO thereby represents a solid foundation for differential diagnostic applications as well as for translational research and prioritization of novel disease genes in exome or genome sequencing projects.
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Affiliation(s)
- Sebastian Köhler
- NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, 06032, Farmington, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, USA
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Cipriani V, Kalhoro A, Arno G, Silva RS, Pontikos N, Puech V, McClements ME, Hunt DM, van Heyningen V, Michaelides M, Webster AR, Moore AT, Puech B. Genome-wide linkage and haplotype sharing analysis implicates the MCDR3 locus as a candidate region for a developmental macular disorder in association with digit abnormalities. Ophthalmic Genet 2017. [DOI: 10.1080/13816810.2017.1289544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Valentina Cipriani
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Ambreen Kalhoro
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Raquel S. Silva
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Nikolas Pontikos
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Michelle E. McClements
- Nuffield Department of Clinical Neurosciences (Ophthalmology), University of Oxford, Oxford, UK
| | - David M. Hunt
- Lions Eye Institute and School of Animal Biology, University of Western Australia, Perth, Western Australia, Australia
| | - Veronica van Heyningen
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
| | - Michel Michaelides
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Andrew R. Webster
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Anthony T. Moore
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
- Ophthalmology Department, University of California, San Francisco School of Medicine, San Francisco, California, USA
| | - Bernard Puech
- Service d’Exploration de la Vision CHU, Lille, France
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D'Souza M, Sulakhe D, Wang S, Xie B, Hashemifar S, Taylor A, Dubchak I, Conrad Gilliam T, Maltsev N. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks. Methods Mol Biol 2017; 1613:85-99. [PMID: 28849559 DOI: 10.1007/978-1-4939-7027-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.
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Affiliation(s)
- Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.
- Argonne National Laboratory, Building 221, Room: A142, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Bing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Somaye Hashemifar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Andrew Taylor
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
| | - Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
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Jäger M, Schubach M, Zemojtel T, Reinert K, Church DM, Robinson PN. Alternate-locus aware variant calling in whole genome sequencing. Genome Med 2016; 8:130. [PMID: 27964746 PMCID: PMC5155401 DOI: 10.1186/s13073-016-0383-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/23/2016] [Indexed: 01/09/2023] Open
Abstract
Background The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. The new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS). Methods We developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions. We investigate 121 in-house WGS datasets that have been aligned to the GRCh37 and GRCh38 assemblies. Results We show that stretches of sequences that are largely but not entirely identical between the primary assembly and an alternate locus can result in multiple variant calls against regions of the primary assembly. In WGS analysis, this results in characteristic and recognizable patterns of variant calls at positions that we term alignable scaffold-discrepant positions (ASDPs). In 121 in-house genomes, on average 51.8±3.8 of the 178 regions were found to correspond best to an alternate locus rather than the primary assembly sequence, and filtering these genomes with our algorithm led to the identification of 7863 variant calls per genome that colocalized with ASDPs. Additionally, we found that 437 of 791 genome-wide association study hits located within one of the regions corresponded to ASDPs. Conclusions Our algorithm uses the information contained in the 178 structurally variable regions of the GRCh38 genome assembly to avoid spurious variant calls in cases where samples contain an alternate locus rather than the corresponding segment of the primary assembly. These results suggest the great potential of fully incorporating the resources of graph-like genome assemblies into variant calling, but also underscore the importance of developing computational resources that will allow a full reconstruction of the genotype in personal genomes. Our algorithm is freely available at https://github.com/charite/asdpex. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0383-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marten Jäger
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Max Schubach
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Tomasz Zemojtel
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Knut Reinert
- Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany
| | - Deanna M Church
- 10x Genomics, 7068 Koll Center Parkway, Suite 401, Pleasanton, 94566, CA, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany. .,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany. .,Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. .,The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, 06032, CT, USA. .,Institute for Systems Genomics, University of Connecticut, Farmington, 06032, CT, USA.
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42
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Smedley D, Schubach M, Jacobsen J, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington N, McMurry J, Haendel M, Mungall C, Lewis S, Groza T, Valentini G, Robinson P. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet 2016; 99:595-606. [PMID: 27569544 DOI: 10.1016/j.ajhg.2016.07.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/01/2016] [Indexed: 12/17/2022] Open
Abstract
The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Overall, Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease.
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43
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016; 135:603-14. [PMID: 27075447 PMCID: PMC4883269 DOI: 10.1007/s00439-016-1658-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/15/2016] [Indexed: 01/19/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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44
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016. [PMID: 27075447 DOI: 10.1007/s00439‐016‐1658‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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Parenti I, Gervasini C, Pozojevic J, Wendt KS, Watrin E, Azzollini J, Braunholz D, Buiting K, Cereda A, Engels H, Garavelli L, Glazar R, Graffmann B, Larizza L, Lüdecke HJ, Mariani M, Masciadri M, Pié J, Ramos FJ, Russo S, Selicorni A, Stefanova M, Strom TM, Werner R, Wierzba J, Zampino G, Gillessen-Kaesbach G, Wieczorek D, Kaiser FJ. Expanding the clinical spectrum of the 'HDAC8-phenotype' - implications for molecular diagnostics, counseling and risk prediction. Clin Genet 2016; 89:564-73. [PMID: 26671848 DOI: 10.1111/cge.12717] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/30/2015] [Accepted: 12/12/2015] [Indexed: 01/25/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically heterogeneous disorder characterized by typical facial dysmorphism, cognitive impairment and multiple congenital anomalies. Approximately 75% of patients carry a variant in one of the five cohesin-related genes NIPBL, SMC1A, SMC3, RAD21 and HDAC8. Herein we report on the clinical and molecular characterization of 11 patients carrying 10 distinct variants in HDAC8. Given the high number of variants identified so far, we advise sequencing of HDAC8 as an indispensable part of the routine molecular diagnostic for patients with CdLS or CdLS-overlapping features. The phenotype of our patients is very broad, whereas males tend to be more severely affected than females, who instead often present with less canonical CdLS features. The extensive clinical variability observed in the heterozygous females might be at least partially associated with a completely skewed X-inactivation, observed in seven out of eight female patients. Our cohort also includes two affected siblings whose unaffected mother was found to be mosaic for the causative mutation inherited to both affected children. This further supports the urgent need for an integration of highly sensitive sequencing technology to allow an appropriate molecular diagnostic, genetic counseling and risk prediction.
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Affiliation(s)
- I Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany.,Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - C Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - J Pozojevic
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - E Watrin
- Faculté de Médecine, Institut de Génétique et Développement de Rennes, UMR6290-CNRS, Rennes, France
| | - J Azzollini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - D Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K Buiting
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - A Cereda
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - H Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - L Garavelli
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, IRCCS S. Maria Nuova Hospital, Reggio Emilia, Italy
| | - R Glazar
- The Center for Medical Genetics GENESIS Poznan, Poland
| | - B Graffmann
- Department of Pediatrics, University Hospital Linköping, Linköping, Sweden
| | - L Larizza
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - H J Lüdecke
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - M Mariani
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Masciadri
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - F J Ramos
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain.,Unidad de Genetica Clınica, Servicio de Pediatrıa, Hospital Clınico Universitario "Lozano Blesa", CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - S Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - A Selicorni
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - T M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - R Werner
- Division of Experimental Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany
| | - J Wierzba
- Department and Clinic of Pediatrics, Hematooncology, Oncology and Endocrinology, Medical University of Gdańsk, Gdańsk, Poland.,Department of General Nursing, Medical University of Gdańsk, Gdańsk, Poland
| | - G Zampino
- Birth Defects Unit, Department of Pediatrics, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - D Wieczorek
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - F J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
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Zhu N, Heinrich V, Dickhaus T, Hecht J, Robinson PN, Mundlos S, Kamphans T, Krawitz PM. Strategies to improve the performance of rare variant association studies by optimizing the selection of controls. Bioinformatics 2015; 31:3577-83. [PMID: 26249812 DOI: 10.1093/bioinformatics/btv457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/30/2015] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION When analyzing a case group of patients with ultra-rare disorders the ethnicities are often diverse and the data quality might vary. The population substructure in the case group as well as the heterogeneous data quality can cause substantial inflation of test statistics and result in spurious associations in case-control studies if not properly adjusted for. Existing techniques to correct for confounding effects were especially developed for common variants and are not applicable to rare variants. RESULTS We analyzed strategies to select suitable controls for cases that are based on similarity metrics that vary in their weighting schemes. We simulated different disease entities on real exome data and show that a similarity-based selection scheme can help to reduce false positive associations and to optimize the performance of the statistical tests. Especially when data quality as well as ethnicities vary a lot in the case group, a matching approach that puts more weight on rare variants shows the best performance. We reanalyzed collections of unrelated patients with Kabuki make-up syndrome, Hyperphosphatasia with Mental Retardation syndrome and Catel-Manzke syndrome for which the disease genes were recently described. We show that rare variant association tests are more sensitive and specific in identifying the disease gene than intersection filters and should thus be considered as a favorable approach in analyzing even small patient cohorts. AVAILABILITY AND IMPLEMENTATION Datasets used in our analysis are available at ftp://ftp.1000genomes.ebi.ac.uk./vol1/ftp/ CONTACT : peter.krawitz@charite.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Na Zhu
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Thorsten Dickhaus
- Institute for Statistics, University of Bremen, 28344 Bremen, Germany
| | - Jochen Hecht
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Peter N Robinson
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany and
| | | | - Peter M Krawitz
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany and
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Smedley D, Jacobsen JOB, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat Protoc 2015; 10:2004-15. [PMID: 26562621 DOI: 10.1038/nprot.2015.124] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Exomiser is an application that prioritizes genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser comprises a suite of algorithms for prioritizing exome sequences using random-walk analysis of protein interaction networks, clinical relevance and cross-species phenotype comparisons, as well as a wide range of other computational filters for variant frequency, predicted pathogenicity and pedigree analysis. In this protocol, we provide a detailed explanation of how to install Exomiser and use it to prioritize exome sequences in a number of scenarios. Exomiser requires ∼3 GB of RAM and roughly 15-90 s of computing time on a standard desktop computer to analyze a variant call format (VCF) file. Exomiser is freely available for academic use from http://www.sanger.ac.uk/science/tools/exomiser.
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Affiliation(s)
- Damian Smedley
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Marten Jäger
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute for Health, Berlin, Germany
| | - Max Schubach
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Enrico Siragusa
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute for Health, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tomasz Zemojtel
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Labor Berlin - Charité Vivantes, Humangenetik, Berlin, Germany
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicole L Washington
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William P Bone
- The National Institutes of Health (NIH) Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health &Science University, Portland, Oregon, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Berlin, Germany
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Yang H, Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods 2015; 12:841-3. [PMID: 26192085 PMCID: PMC4718403 DOI: 10.1038/nmeth.3484] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 12/21/2022]
Abstract
Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.
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Affiliation(s)
- Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, California, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
- Department of Psychiatry, University of Southern California, Los Angeles, California, USA
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
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Goyal S, Jäger M, Robinson PN, Vanita V. Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51). Clin Genet 2015. [PMID: 26195043 DOI: 10.1111/cge.12644] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nonsyndromic retinitis pigmentosa (RP) is genetically highly heterogeneous, with >100 disease genes identified. However, mutations in these genes explain only 60% of all RP cases. Blood samples were collected from 12 members of an autosomal recessive RP family. Whole genome homozygosity mapping and haplotype analysis placed the RP locus in this family at chromosome 14q31.3. Whole-exome sequencing (WES) in proband revealed a mutation in TTC8, which was flagged as most likely candidate gene by bioinformatic analysis. TTC8 is mutated in Bardet-Biedl syndrome 8 (BBS8), and once reported previously in a family with nonsyndromic RP. Sequencing of amplified products of exon 13 of TTC8 validated c.1347G>C (p.Gln449His), a novel change that affects the final nucleotide of exon 13 and might deleteriously affect splicing. This mutation segregated completely with the disease in the family and was not observed in 100 ethnically matched controls from same population. This represents second report of a TTC8 mutation in nonsyndromic RP, thus confirming the identity of TTC8 as causative gene for RP51.
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Affiliation(s)
- S Goyal
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - M Jäger
- Institute for Medical and Human Genetics, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - P N Robinson
- Institute for Medical and Human Genetics, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - V Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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