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Lesmann H, Hustinx A, Moosa S, Klinkhammer H, Marchi E, Caro P, Abdelrazek IM, Pantel JT, Hagen MT, Thong MK, Binti Mazlan RA, Tae SK, Kamphans T, Meiswinkel W, Li JM, Javanmardi B, Knaus A, Uwineza A, Knopp C, Tkemaladze T, Elbracht M, Mattern L, Jamra RA, Velmans C, Strehlow V, Jacob M, Peron A, Dias C, Nunes BC, Vilella T, Pinheiro IF, Kim CA, Melaragno MI, Weiland H, Kaptain S, Chwiałkowska K, Kwasniewski M, Saad R, Wiethoff S, Goel H, Tang C, Hau A, Barakat TS, Panek P, Nabil A, Suh J, Braun F, Gomy I, Averdunk L, Ekure E, Bergant G, Peterlin B, Graziano C, Gaboon N, Fiesco-Roa M, Spinelli AM, Wilpert NM, Phowthongkum P, Güzel N, Haack TB, Bitar R, Tzschach A, Rodriguez-Palmero A, Brunet T, Rudnik-Schöneborn S, Contreras-Capetillo SN, Oberlack A, Samango-Sprouse C, Sadeghin T, Olaya M, Platzer K, Borovikov A, Schnabel F, Heuft L, Herrmann V, Oegema R, Elkhateeb N, Kumar S, Komlosi K, Mohamed K, Kalantari S, Sirchia F, Martinez-Monseny AF, Höller M, Toutouna L, Mohamed A, Lasa-Aranzasti A, Sayer JA, Ehmke N, Danyel M, Sczakiel H, Schwartzmann S, Boschann F, Zhao M, Adam R, Einicke L, Horn D, Chew KS, KAM CC, Karakoyun M, Pode-Shakked B, Eliyahu A, Rock R, Carrion T, Chorin O, Zarate YA, Conti MM, Karakaya M, Tung ML, Chandra B, Bouman A, Lumaka A, Wasif N, Shinawi M, Blackburn PR, Wang T, Niehues T, Schmidt A, Roth RR, Wieczorek D, Hu P, Waikel RL, Ledgister Hanchard SE, Elmakkawy G, Safwat S, Ebstein F, Krüger E, Küry S, Bézieau S, Arlt A, Olinger E, Marbach F, Li D, Dupuis L, Mendoza-Londono R, Houge SD, Weis D, Chung BHY, Mak CC, Kayserili H, Elcioglu N, Aykut A, Şimşek-Kiper PÖ, Bögershausen N, Wollnik B, Bentzen HB, Kurth I, Netzer C, Jezela-Stanek A, Devriendt K, Gripp KW, Mücke M, Verloes A, Schaaf CP, Nellåker C, Solomon BD, Nöthen MM, Abdalla E, Lyon GJ, Krawitz PM, Hsieh TC. GestaltMatcher Database - A global reference for facial phenotypic variability in rare human diseases. RESEARCH SQUARE 2024:rs.3.rs-4438861. [PMID: 38903062 PMCID: PMC11188141 DOI: 10.21203/rs.3.rs-4438861/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The most important factor that complicates the work of dysmorphologists is the significant phenotypic variability of the human face. Next-Generation Phenotyping (NGP) tools that assist clinicians with recognizing characteristic syndromic patterns are particularly challenged when confronted with patients from populations different from their training data. To that end, we systematically analyzed the impact of genetic ancestry on facial dysmorphism. For that purpose, we established the GestaltMatcher Database (GMDB) as a reference dataset for medical images of patients with rare genetic disorders from around the world. We collected 10,980 frontal facial images - more than a quarter previously unpublished - from 8,346 patients, representing 581 rare disorders. Although the predominant ancestry is still European (67%), data from underrepresented populations have been increased considerably via global collaborations (19% Asian and 7% African). This includes previously unpublished reports for more than 40% of the African patients. The NGP analysis on this diverse dataset revealed characteristic performance differences depending on the composition of training and test sets corresponding to genetic relatedness. For clinical use of NGP, incorporating non-European patients resulted in a profound enhancement of GestaltMatcher performance. The top-5 accuracy rate increased by +11.29%. Importantly, this improvement in delineating the correct disorder from a facial portrait was achieved without decreasing the performance on European patients. By design, GMDB complies with the FAIR principles by rendering the curated medical data findable, accessible, interoperable, and reusable. This means GMDB can also serve as data for training and benchmarking. In summary, our study on facial dysmorphism on a global sample revealed a considerable cross ancestral phenotypic variability confounding NGP that should be counteracted by international efforts for increasing data diversity. GMDB will serve as a vital reference database for clinicians and a transparent training set for advancing NGP technology.
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Affiliation(s)
- Hellen Lesmann
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Stellenbosch, South Africa
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, NRW, Germany
| | - Elaine Marchi
- New York State Institute for Basic Research in Developmental Disabilities, New York State, Albany, New York, USA
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Ibrahim M. Abdelrazek
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Jean Tori Pantel
- Institute for Digitalization and General Medicine, University Hospital RWTH Aachen, Aachen, NRW, Germany
- Centre for Rare Diseases Aachen (ZSEA), University Hospital RWTH Aachen, Aachen, NRW, Germany
| | - Merle ten Hagen
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Meow-Keong Thong
- Department of Paediatrics, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Sok Kun Tae
- Department of Paediatrics, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Jing-Mei Li
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Behnam Javanmardi
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Annette Uwineza
- College of Medicine and Health Sciences, University of Rwanda, and University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- Givi Zhvania Pediatric Academic Clinic, Tbilisi State Medical University, Georgia
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Larissa Mattern
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Clara Velmans
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Angela Peron
- Medical Genetics, Meyer Children’s Hospital IRCCS, Firenze, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Università degli Studi di Firenze, Italy
| | - Cristina Dias
- Department of Medical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, UK
- Department of Medical & Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, UK
| | - Beatriz Carvalho Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Thainá Vilella
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Chong Ae Kim
- Genetics Unit, Instituto da Criança, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Hannah Weiland
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Sophia Kaptain
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- IMAGENE.ME SA, Bialystok, Poland
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- IMAGENE.ME SA, Bialystok, Poland
| | - Ramy Saad
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London UK
| | - Sarah Wiethoff
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, NRW, Germany
| | - Himanshu Goel
- School of Medicine and Public Health, University of Newcastle, Callaghan NSW, Australia
| | - Clara Tang
- Kabuki Syndrome Foundation, Northbrook, IL, USA
| | - Anna Hau
- Hunter Genetics, Hunter New England Health Service, Newcastle, Australia
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Przemysław Panek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Julia Suh
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Frederik Braun
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, NRW, Germany
| | - Israel Gomy
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Sao Paulo, Brazil
| | - Luisa Averdunk
- Department of General Pediatrics and Neonatology, University Children’s Hospital, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Ekanem Ekure
- Department of Paediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana
| | | | - Nagwa Gaboon
- Medical Genetics Center, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Medical Genetics Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Moisés Fiesco-Roa
- Programa de Maestría y Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México, México City, Mexico
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México City, Mexico
| | | | - Nina-Maria Wilpert
- NeuroCure Cluster of Excellence; Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, D-10117 Berlin, Germany
- Department of Neuropediatrics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, D-13353 Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, D-10117 Berlin, German
| | - Prasit Phowthongkum
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
- Division of Medical Genetics and Genomics, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nergis Güzel
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rana Bitar
- Pediatric Gastroenterology Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
- Khalifa University, Abu Dhabi, United Arab Emirates
| | - Andreas Tzschach
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Agusti Rodriguez-Palmero
- Paediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | | | | | - Ava Oberlack
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Carole Samango-Sprouse
- Department of Pediatrics, George Washington University, 2121 I St. NW, Washington D.C. 2005
- Department of Human and Molecular Genetics, Florida International University, 11200 SW 8th Street, AHC2 Miami, Florida 22199
- Department of Research, The Focus Foundation, 820 W. Central Ave. #190, Davidsonville, MD 21035
| | - Teresa Sadeghin
- Department of Research, The Focus Foundation, 2772 Rutland Road P.O. Box 190, Davidsonville, MD 21035
| | - Margaret Olaya
- Department of Research, The Focus Foundation, 2772 Rutland Road P.O. Box 190, Davidsonville, MD 21035
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Franziska Schnabel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Lara Heuft
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vera Herrmann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nour Elkhateeb
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Katalin Komlosi
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Khoushoua Mohamed
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Silvia Kalantari
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Antonio F. Martinez-Monseny
- Department of Clinical Genetics, SJD Barcelona Children’s Hospital, Esplugues del Llobregat (Barcelona), Spain
| | - Matthias Höller
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Louiza Toutouna
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Amal Mohamed
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, Barcelona, Catalunya, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, Barcelona, Catalunya, Spain
| | - John A. Sayer
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
- Renal Services, The Newcastle Upon Tyne NHS Hospitals Foundation Trust, Freeman Road, Newcastle Upon Tyne, UK
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Henrike Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Max Zhao
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Choy Chen KAM
- Department of Paediatrics, Faculty of Medicine, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Miray Karakoyun
- Ege University, Faculty of Medicine, Department of Pediatric Gastroenterology Hepatology and Nutrition, Izmir, Turkey
| | - Ben Pode-Shakked
- The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- The faculty of Medical and Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rachel Rock
- Metabolic Diseases Clinic, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center
- National Newborn Screening Program, Public Health Services, Ministry of Health Tel-Hashomer, Israel
| | - Teresa Carrion
- Rare diseases Unit, Pediatric Department, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Odelia Chorin
- The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yuri A. Zarate
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, AR, USA
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | | | - Mert Karakaya
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Moon Ley Tung
- University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Bharatendu Chandra
- University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Aime Lumaka
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo
| | - Naveed Wasif
- Institute of Human Genetics, University of Ulm, Ulm, Baden-Württemberg, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick R. Blackburn
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing 100191, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing 100191, China
- Autism Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Tim Niehues
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Regina Rita Roth
- Institute of Human Genetics, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Ping Hu
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | - Rebekah L. Waikel
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | | | - Gehad Elmakkawy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Sylvia Safwat
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Frédéric Ebstein
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Elke Krüger
- Insitute for Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald, Greifswald, Germany
| | - Sébastien Küry
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Annabelle Arlt
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Eric Olinger
- Center for Human Genetics, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Felix Marbach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Dong Li
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lucie Dupuis
- Department to Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital of Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Department to Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital of Sick Children, Toronto, Ontario, Canada
| | - Sofia Douzgou Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Denisa Weis
- Institue for Medical Genetics, Kepler University Hospital, Linz, Austria
| | - Brian Hon-Yin Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher C.Y. Mak
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSoM), 34010, Istanbul, Türkiye
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University School of Medicine, Istanbul, Türkiye
| | - Ayca Aykut
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Türkiye
| | | | - Nina Bögershausen
- Institut of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institut of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Christian Netzer
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | | | - Karen W. Gripp
- Division of Medical Genetics, A.I. du Pont Hospital for Children/Nemours, USA, Wilmington, Delaware, USA
| | - Martin Mücke
- Institute for Digitalization and General Medicine, University Hospital RWTH Aachen, Aachen, NRW, Germany
- Centre for Rare Diseases Aachen (ZSEA), University Hospital RWTH Aachen, Aachen, NRW, Germany
| | - Alain Verloes
- Department of Clinical Genetics, Robert-Debré Hospital, Paris, France
| | - Christian P. Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Christoffer Nellåker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, UK
| | - Benjamin D. Solomon
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Gholson J. Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
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Lesmann H, Hustinx A, Moosa S, Klinkhammer H, Marchi E, Caro P, Abdelrazek IM, Pantel JT, Ten Hagen M, Thong MK, Binti Mazlan RA, Tae SK, Kamphans T, Meiswinkel W, Li JM, Javanmardi B, Knaus A, Uwineza A, Knopp C, Tkemaladze T, Elbracht M, Mattern L, Jamra RA, Velmans C, Strehlow V, Jacob M, Peron A, Dias C, Nunes BC, Vilella T, Pinheiro IF, Kim CA, Melaragno MI, Weiland H, Kaptain S, Chwiałkowska K, Kwasniewski M, Saad R, Wiethoff S, Goel H, Tang C, Hau A, Barakat TS, Panek P, Nabil A, Suh J, Braun F, Gomy I, Averdunk L, Ekure E, Bergant G, Peterlin B, Graziano C, Gaboon N, Fiesco-Roa M, Spinelli AM, Wilpert NM, Phowthongkum P, Güzel N, Haack TB, Bitar R, Tzschach A, Rodriguez-Palmero A, Brunet T, Rudnik-Schöneborn S, Contreras-Capetillo SN, Oberlack A, Samango-Sprouse C, Sadeghin T, Olaya M, Platzer K, Borovikov A, Schnabel F, Heuft L, Herrmann V, Oegema R, Elkhateeb N, Kumar S, Komlosi K, Mohamed K, Kalantari S, Sirchia F, Martinez-Monseny AF, Höller M, Toutouna L, Mohamed A, Lasa-Aranzasti A, Sayer JA, Ehmke N, Danyel M, Sczakiel H, Schwartzmann S, Boschann F, Zhao M, Adam R, Einicke L, Horn D, Chew KS, Kam CC, Karakoyun M, Pode-Shakked B, Eliyahu A, Rock R, Carrion T, Chorin O, Zarate YA, Conti MM, Karakaya M, Tung ML, Chandra B, Bouman A, Lumaka A, Wasif N, Shinawi M, Blackburn PR, Wang T, Niehues T, Schmidt A, Roth RR, Wieczorek D, Hu P, Waikel RL, Ledgister Hanchard SE, Elmakkawy G, Safwat S, Ebstein F, Krüger E, Küry S, Bézieau S, Arlt A, Olinger E, Marbach F, Li D, Dupuis L, Mendoza-Londono R, Houge SD, Weis D, Chung BHY, Mak CCY, Kayserili H, Elcioglu N, Aykut A, Şimşek-Kiper PÖ, Bögershausen N, Wollnik B, Bentzen HB, Kurth I, Netzer C, Jezela-Stanek A, Devriendt K, Gripp KW, Mücke M, Verloes A, Schaaf CP, Nellåker C, Solomon BD, Nöthen MM, Abdalla E, Lyon GJ, Krawitz PM, Hsieh TC. GestaltMatcher Database - A global reference for facial phenotypic variability in rare human diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.06.06.23290887. [PMID: 37503210 PMCID: PMC10371103 DOI: 10.1101/2023.06.06.23290887] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The most important factor that complicates the work of dysmorphologists is the significant phenotypic variability of the human face. Next-Generation Phenotyping (NGP) tools that assist clinicians with recognizing characteristic syndromic patterns are particularly challenged when confronted with patients from populations different from their training data. To that end, we systematically analyzed the impact of genetic ancestry on facial dysmorphism. For that purpose, we established the GestaltMatcher Database (GMDB) as a reference dataset for medical images of patients with rare genetic disorders from around the world. We collected 10,980 frontal facial images - more than a quarter previously unpublished - from 8,346 patients, representing 581 rare disorders. Although the predominant ancestry is still European (67%), data from underrepresented populations have been increased considerably via global collaborations (19% Asian and 7% African). This includes previously unpublished reports for more than 40% of the African patients. The NGP analysis on this diverse dataset revealed characteristic performance differences depending on the composition of training and test sets corresponding to genetic relatedness. For clinical use of NGP, incorporating non-European patients resulted in a profound enhancement of GestaltMatcher performance. The top-5 accuracy rate increased by +11.29%. Importantly, this improvement in delineating the correct disorder from a facial portrait was achieved without decreasing the performance on European patients. By design, GMDB complies with the FAIR principles by rendering the curated medical data findable, accessible, interoperable, and reusable. This means GMDB can also serve as data for training and benchmarking. In summary, our study on facial dysmorphism on a global sample revealed a considerable cross ancestral phenotypic variability confounding NGP that should be counteracted by international efforts for increasing data diversity. GMDB will serve as a vital reference database for clinicians and a transparent training set for advancing NGP technology.
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Affiliation(s)
- Hellen Lesmann
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Stellenbosch, South Africa
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, NRW, Germany
| | - Elaine Marchi
- New York State Institute for Basic Research in Developmental Disabilities, New York State, Albany, New York, USA
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Ibrahim M Abdelrazek
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Jean Tori Pantel
- Institute for Digitalization and General Medicine, University Hospital RWTH Aachen, Aachen, NRW, Germany
- Centre for Rare Diseases Aachen (ZSEA), University Hospital RWTH Aachen, Aachen, NRW, Germany
| | - Merle Ten Hagen
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Meow-Keong Thong
- Department of Paediatrics, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Sok Kun Tae
- Department of Paediatrics, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Jing-Mei Li
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Behnam Javanmardi
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Annette Uwineza
- College of Medicine and Health Sciences, University of Rwanda, and University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- Givi Zhvania Pediatric Academic Clinic, Tbilisi State Medical University, Georgia
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Larissa Mattern
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Clara Velmans
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Angela Peron
- Medical Genetics, Meyer Children's Hospital IRCCS, Firenze, Italy
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università degli Studi di Firenze, Italy
| | - Cristina Dias
- Department of Medical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, UK
- Department of Medical & Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, UK
| | - Beatriz Carvalho Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Thainá Vilella
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Chong Ae Kim
- Genetics Unit, Instituto da Criança, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Hannah Weiland
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Sophia Kaptain
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- IMAGENE.ME SA, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Ramy Saad
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London UK
| | - Sarah Wiethoff
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, NRW, Germany
| | - Himanshu Goel
- School of Medicine and Public Health, University of Newcastle, Callaghan NSW, Australia
| | - Clara Tang
- Kabuki Syndrome Foundation, Northbrook, IL, USA
| | - Anna Hau
- Hunter Genetics, Hunter New England Health Service, Newcastle, Australia
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Przemysław Panek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Julia Suh
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Frederik Braun
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, NRW, Germany
| | - Israel Gomy
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Sao Paulo, Brazil
| | - Luisa Averdunk
- Department of General Pediatrics and Neonatology, University Children's Hospital, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Ekanem Ekure
- Department of Paediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana
| | | | - Nagwa Gaboon
- Medical Genetics Center, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Medical Genetics Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Moisés Fiesco-Roa
- Programa de Maestría y Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México, México City, Mexico
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México City, Mexico
| | | | - Nina Maria Wilpert
- NeuroCure Cluster of Excellence; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, D-10117 Berlin, Germany
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, D-13353 Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, D-10117 Berlin, German
| | - Prasit Phowthongkum
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
- Division of Medical Genetics and Genomics, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nergis Güzel
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rana Bitar
- Pediatric Gastroenterology Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
- Khalifa University, Abu Dhabi, United Arab Emirates
| | - Andreas Tzschach
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Agusti Rodriguez-Palmero
- Paediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat AutÓnoma de Barcelona, Barcelona, Spain
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | | | | | - Ava Oberlack
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Carole Samango-Sprouse
- Department of Pediatrics, George Washington University, 2121 I St. NW, Washington D.C. 2005
- Department of Human and Molecular Genetics, Florida International University, 11200 SW 8th Street, AHC2 Miami, Florida 22199
- Department of Research, The Focus Foundation, 820 W. Central Ave. #190, Davidsonville, MD 21035
| | - Teresa Sadeghin
- Department of Research, The Focus Foundation, 2772 Rutland Road P.O. Box 190, Davidsonville, MD 21035
| | - Margaret Olaya
- Department of Research, The Focus Foundation, 2772 Rutland Road P.O. Box 190, Davidsonville, MD 21035
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Franziska Schnabel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Lara Heuft
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vera Herrmann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nour Elkhateeb
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Katalin Komlosi
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Khoushoua Mohamed
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Silvia Kalantari
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Antonio F Martinez-Monseny
- Department of Clinical Genetics, SJD Barcelona Children's Hospital, Esplugues del Llobregat (Barcelona), Spain
| | - Matthias Höller
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Louiza Toutouna
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Amal Mohamed
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Catalunya, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Catalunya, Spain
| | - John A Sayer
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
- Renal Services, The Newcastle Upon Tyne NHS Hospitals Foundation Trust, Freeman Road, Newcastle Upon Tyne, UK
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Henrike Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Max Zhao
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Choy Chen Kam
- Department of Paediatrics, Faculty of Medicine, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Miray Karakoyun
- Ege University, Faculty of Medicine, Department of Pediatric Gastroenterology Hepatology and Nutrition, Izmir, Turkey
| | - Ben Pode-Shakked
- The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- The faculty of Medical and Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rachel Rock
- Metabolic Diseases Clinic, Edmond and Lily Safra Children's Hospital, Sheba Medical Center
- National Newborn Screening Program, Public Health Services, Ministry of Health Tel-Hashomer, Israel
| | - Teresa Carrion
- Rare diseases Unit, Pediatric Department, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Odelia Chorin
- The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yuri A Zarate
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, USA
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | | | - Mert Karakaya
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Moon Ley Tung
- University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Bharatendu Chandra
- University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Aime Lumaka
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo
| | - Naveed Wasif
- Institute of Human Genetics, University of Ulm, Ulm, Baden-Württemberg, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing 100191, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing 100191, China
- Autism Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Tim Niehues
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Regina Rita Roth
- Institute of Human Genetics, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Ping Hu
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | - Rebekah L Waikel
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | | | - Gehad Elmakkawy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Sylvia Safwat
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Frédéric Ebstein
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Elke Krüger
- Insitute for Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald, Greifswald, Germany
| | - Sébastien Küry
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, F-44000 Nantes, France
| | - Annabelle Arlt
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Eric Olinger
- Center for Human Genetics, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Felix Marbach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Dong Li
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lucie Dupuis
- Department to Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital of Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Department to Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital of Sick Children, Toronto, Ontario, Canada
| | - Sofia Douzgou Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Denisa Weis
- Institue for Medical Genetics, Kepler University Hospital, Linz, Austria
| | - Brian Hon-Yin Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSoM), 34010, Istanbul, Türkiye
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University School of Medicine, Istanbul, Türkiye
| | - Ayca Aykut
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Türkiye
| | | | - Nina Bögershausen
- Institut of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institut of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, NRW, Germany
| | - Christian Netzer
- Institute of Human Genetics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, Germany
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | | | - Karen W Gripp
- Division of Medical Genetics, A.I. du Pont Hospital for Children/Nemours, USA, Wilmington, Delaware, USA
| | - Martin Mücke
- Institute for Digitalization and General Medicine, University Hospital RWTH Aachen, Aachen, NRW, Germany
- Centre for Rare Diseases Aachen (ZSEA), University Hospital RWTH Aachen, Aachen, NRW, Germany
| | - Alain Verloes
- Department of Clinical Genetics, Robert-Debré Hospital, Paris, France
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Christoffer Nellåker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Benjamin D Solomon
- Medical Genomics Unit, Medical Genetics Branch, National Human Genome Research Institute, Bethesda, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, NRW, Germany
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Alexandria, Egypt
| | - Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, NRW, Germany
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Liu Y, Xia D, Zhong L, Chen L, Zhang L, Ai M, Mei R, Pang R. Casein Kinase 2 Affects Epilepsy by Regulating Ion Channels: A Potential Mechanism. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:894-905. [PMID: 37350003 DOI: 10.2174/1871527322666230622124618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 06/24/2023]
Abstract
Epilepsy, characterized by recurrent seizures and abnormal brain discharges, is the third most common chronic disorder of the Central Nervous System (CNS). Although significant progress has been made in the research on antiepileptic drugs (AEDs), approximately one-third of patients with epilepsy are refractory to these drugs. Thus, research on the pathogenesis of epilepsy is ongoing to find more effective treatments. Many pathological mechanisms are involved in epilepsy, including neuronal apoptosis, mossy fiber sprouting, neuroinflammation, and dysfunction of neuronal ion channels, leading to abnormal neuronal excitatory networks in the brain. CK2 (Casein kinase 2), which plays a critical role in modulating neuronal excitability and synaptic transmission, has been shown to be associated with epilepsy. However, there is limited research on the mechanisms involved. Recent studies have suggested that CK2 is involved in regulating the function of neuronal ion channels by directly phosphorylating them or their binding partners. Therefore, in this review, we will summarize recent research advances regarding the potential role of CK2 regulating ion channels in epilepsy, aiming to provide more evidence for future studies.
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Affiliation(s)
- Yan Liu
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Di Xia
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Lianmei Zhong
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Ling Chen
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, 650032, China
| | - Linming Zhang
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Mingda Ai
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Rong Mei
- Department of Neurology, the First People's Hospital of Yunnan Province, Kunming, Yunnan, 650034, China
| | - Ruijing Pang
- Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
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Hsieh TC, Lesmann H, Krawitz PM. Facilitating the Molecular Diagnosis of Rare Genetic Disorders Through Facial Phenotypic Scores. Curr Protoc 2023; 3:e906. [PMID: 37812136 DOI: 10.1002/cpz1.906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
With recent advances in computer vision, many applications based on artificial intelligence have been developed to facilitate the diagnosis of rare genetic disorders through the analysis of patients' two-dimensional frontal images. Some of these have been implemented on online platforms with user-friendly interfaces and provide facial analysis services, such as Face2Gene. However, users cannot run the facial analysis processes in house because the training data and the trained models are unavailable. This article therefore provides an introduction, designed for users with programming backgrounds, to the use of the open-source GestaltMatcher approach to run facial analysis in their local environment. The Basic Protocol provides detailed instructions for applying for access to the trained models and then performing facial analysis to obtain a prediction score for each of the 595 genes in the GestaltMatcher Database. The prediction results can then be used to narrow down the search space of disease-causing mutations or further connect with a variant-prioritization pipeline. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Using the open-source GestaltMatcher approach to perform facial analysis.
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Affiliation(s)
- Tzung-Chien Hsieh
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hellen Lesmann
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institut für Humangenetik, Universitätsklinikum Bonn, Universität Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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5
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Hsieh TC, Krawitz PM. Computational facial analysis for rare Mendelian disorders. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:e32061. [PMID: 37584245 DOI: 10.1002/ajmg.c.32061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
With the advances in computer vision, computational facial analysis has become a powerful and effective tool for diagnosing rare disorders. This technology, also called next-generation phenotyping (NGP), has progressed significantly over the last decade. This review paper will introduce three key NGP approaches. In 2014, Ferry et al. first presented Clinical Face Phenotype Space (CFPS) trained on eight syndromes. After 5 years, Gurovich et al. proposed DeepGestalt, a deep convolutional neural network trained on more than 21,000 patient images with 216 disorders. It was considered a state-of-the-art disorder classification framework. In 2022, Hsieh et al. developed GestaltMatcher to support the ultra-rare and novel disorders not supported in DeepGestalt. It further enabled the analysis of facial similarity presented in a given cohort or multiple disorders. Moreover, this article will present the usage of NGP for variant prioritization and facial gestalt delineation. Although NGP approaches have proven their capability in assisting the diagnosis of many disorders, many limitations remain. This article will introduce two future directions to address two main limitations: enabling the global collaboration for a medical imaging database that fulfills the FAIR principles and synthesizing patient images to protect patient privacy. In the end, with more and more NGP approaches emerging, we envision that the NGP technology can assist clinicians and researchers in diagnosing patients and analyzing disorders in multiple directions in the near future.
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Affiliation(s)
- Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Moller-Hansen A, Hejla D, Lee HK, Lyles JB, Yang Y, Chen K, Li WL, Thomas G, Boerkoel CF. Do PACS1 variants impeding adaptor protein binding predispose to syndromic intellectual disability? Am J Med Genet A 2023; 191:2181-2187. [PMID: 37141437 PMCID: PMC10524240 DOI: 10.1002/ajmg.a.63232] [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: 01/18/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
To date, PACS1-neurodevelopmental disorder (PACS1-NDD) has been associated with recurrent variation of Arg203 and is considered diagnostic of PACS1-NDD, an autosomal dominant syndromic intellectual disability disorder. Although incompletely defined, the proposed disease mechanism for this variant is altered PACS1 affinity for its client proteins. Given this proposed mechanism, we hypothesized that PACS1 variants that interfere with binding of adaptor proteins might also give rise to syndromic intellectual disability. Herein, we report a proposita and her mother with phenotypic features overlapping PACS1-NDD and a novel PACS1 variant (NM_018026.3:c.[755C > T];[=], p.(Ser252Phe)) that impedes binding of the adaptor protein GGA3 (Golgi-associated, gamma-adaptin ear-containing, ARF-binding protein 3). We hypothesize that attenuating PACS1 binding of GGA3 also gives rise to a disorder with features overlapping those of PACS1-NDD. This observation better delineates the mechanism by which PACS1 variation predisposes to syndromic intellectual disability.
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Affiliation(s)
- Ashley Moller-Hansen
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Duha Hejla
- Department of Pediatrics, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Jenea Barbara Lyles
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yunhan Yang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kun Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cornelius F Boerkoel
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
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Unni P, Friend J, Weinberg J, Okur V, Hochscherf J, Dominguez I. Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases. Front Mol Biosci 2022; 9:851547. [PMID: 36310603 PMCID: PMC9608649 DOI: 10.3389/fmolb.2022.851547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.
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Affiliation(s)
- Prasida Unni
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Jack Friend
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston University, Boston, MA, United States
| | - Volkan Okur
- New York Genome Center, New York, NY, United States
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
- *Correspondence: Isabel Dominguez,
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