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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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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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4
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Hallowell N, Badger S, McKay F, Kerasidou A, Nellåker C. Democratising or disrupting diagnosis? Ethical issues raised by the use of AI tools for rare disease diagnosis. SSM. QUALITATIVE RESEARCH IN HEALTH 2023; 3:100240. [PMID: 37426704 PMCID: PMC10323712 DOI: 10.1016/j.ssmqr.2023.100240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 07/11/2023]
Abstract
Computational phenotyping (CP) technology uses facial recognition algorithms to classify and potentially diagnose rare genetic disorders on the basis of digitised facial images. This AI technology has a number of research as well as clinical applications, such as supporting diagnostic decision-making. Using the example of CP, we examine stakeholders' views of the benefits and costs of using AI as a diagnostic tool within the clinic. Through a series of in-depth interviews (n = 20) with: clinicians, clinical researchers, data scientists, industry and support group representatives, we report stakeholder views regarding the adoption of this technology in a clinical setting. While most interviewees were supportive of employing CP as a diagnostic tool in some capacity we observed ambivalence around the potential for artificial intelligence to overcome diagnostic uncertainty in a clinical context. Thus, while there was widespread agreement amongst interviewees concerning the public benefits of AI assisted diagnosis, namely, its potential to increase diagnostic yield and enable faster more objective and accurate diagnoses by up skilling non specialists and thereby enabling access to diagnosis that is potentially lacking, interviewees also raised concerns about ensuring algorithmic reliability, expunging algorithmic bias and that the use of AI could result in deskilling the specialist clinical workforce. We conclude that, prior to widespread clinical implementation, on-going reflection is needed regarding the trade-offs required to determine acceptable levels of bias and conclude that diagnostic AI tools should only be employed as an assistive technology within the dysmorphology clinic.
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Affiliation(s)
- Nina Hallowell
- The Ethox Centre and Wellcome Centre for Ethics & Humanities, Nuffield Department of Population Health and Big Data Institute, University of Oxford, UK
| | | | - Francis McKay
- The Ethox Centre and Wellcome Centre for Ethics & Humanities, Nuffield Department of Population Health and Big Data Institute, University of Oxford, UK
| | - Angeliki Kerasidou
- The Ethox Centre and Wellcome Centre for Ethics & Humanities, Nuffield Department of Population Health and Big Data Institute, University of Oxford, UK
| | - Christoffer Nellåker
- Nuffield Department of Women's and Reproductive Health and Big Data Institute, University of Oxford, UK
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5
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The ethical and legal landscape of brain data governance. PLoS One 2022; 17:e0273473. [PMID: 36580464 PMCID: PMC9799320 DOI: 10.1371/journal.pone.0273473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
Neuroscience research is producing big brain data which informs both advancements in neuroscience research and drives the development of advanced datasets to provide advanced medical solutions. These brain data are produced under different jurisdictions in different formats and are governed under different regulations. The governance of data has become essential and critical resulting in the development of various governance structures to ensure that the quality, availability, findability, accessibility, usability, and utility of data is maintained. Furthermore, data governance is influenced by various ethical and legal principles. However, it is still not clear what ethical and legal principles should be used as a standard or baseline when managing brain data due to varying practices and evolving concepts. Therefore, this study asks what ethical and legal principles shape the current brain data governance landscape? A systematic scoping review and thematic analysis of articles focused on biomedical, neuro and brain data governance was carried out to identify the ethical and legal principles which shape the current brain data governance landscape. The results revealed that there is currently a large variation of how the principles are presented and discussions around the terms are very multidimensional. Some of the principles are still at their infancy and are barely visible. A range of principles emerged during the thematic analysis providing a potential list of principles which can provide a more comprehensive framework for brain data governance and a conceptual expansion of neuroethics.
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Hallowell N, Badger S, Sauerbrei A, Nellåker C, Kerasidou A. “I don’t think people are ready to trust these algorithms at face value”: trust and the use of machine learning algorithms in the diagnosis of rare disease. BMC Med Ethics 2022; 23:112. [DOI: 10.1186/s12910-022-00842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
As the use of AI becomes more pervasive, and computerised systems are used in clinical decision-making, the role of trust in, and the trustworthiness of, AI tools will need to be addressed. Using the case of computational phenotyping to support the diagnosis of rare disease in dysmorphology, this paper explores under what conditions we could place trust in medical AI tools, which employ machine learning.
Methods
Semi-structured qualitative interviews (n = 20) with stakeholders (clinical geneticists, data scientists, bioinformaticians, industry and patient support group spokespersons) who design and/or work with computational phenotyping (CP) systems. The method of constant comparison was used to analyse the interview data.
Results
Interviewees emphasized the importance of establishing trust in the use of CP technology in identifying rare diseases. Trust was formulated in two interrelated ways in these data. First, interviewees talked about the importance of using CP tools within the context of a trust relationship; arguing that patients will need to trust clinicians who use AI tools and that clinicians will need to trust AI developers, if they are to adopt this technology. Second, they described a need to establish trust in the technology itself, or in the knowledge it provides—epistemic trust. Interviewees suggested CP tools used for the diagnosis of rare diseases might be perceived as more trustworthy if the user is able to vouchsafe for the technology’s reliability and accuracy and the person using/developing them is trusted.
Conclusion
This study suggests we need to take deliberate and meticulous steps to design reliable or confidence-worthy AI systems for use in healthcare. In addition, we need to devise reliable or confidence-worthy processes that would give rise to reliable systems; these could take the form of RCTs and/or systems of accountability transparency and responsibility that would signify the epistemic trustworthiness of these tools. words 294.
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Lucivero F, Hallowell N. Digital/computational phenotyping: What are the differences in the science and the ethics? BIG DATA & SOCIETY 2021; 8:20539517211062885. [PMID: 37790725 PMCID: PMC10544038 DOI: 10.1177/20539517211062885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The concept of 'digital phenotyping' was originally developed by researchers in the mental health field, but it has travelled to other disciplines and areas. This commentary draws upon our experiences of working in two scientific projects that are based at the University of Oxford's Big Data Institute - The RADAR-AD project and The Minerva Initiative - which are developing algorithmic phenotyping technologies. We describe and analyse the concepts of digital biomarkers and computational phenotyping that underlie these projects, explain how they are linked to other research in digital phenotyping and compare and contrast some of their epistemological and ethical implications. In particular, we argue that the phenotyping paradigm in both projects is grounded on an assumption of 'objectivity' that is articulated in different ways depending on the role that is given to the computational/digital tools. Using the concept of 'affordance', we show how specific functionalities relate to potential uses and social implications of these technologies and argue that it is important to distinguish among them as the concept of digital phenotyping is increasingly being used with a variety of meanings.
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Affiliation(s)
- Federica Lucivero
- Ethox Centre and Wellcome Centre for Ethics & Humanities, Nuffield Department of Population Health, University of Oxford, UK
| | - Nina Hallowell
- Ethox Centre and Wellcome Centre for Ethics & Humanities, Nuffield Department of Population Health, University of Oxford, UK
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8
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Quantitative facial phenotyping for Koolen-de Vries and 22q11.2 deletion syndrome. Eur J Hum Genet 2021; 29:1418-1423. [PMID: 33603161 DOI: 10.1038/s41431-021-00824-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/21/2020] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
The Koolen-de Vries syndrome (KdVS) is a multisystem syndrome with variable facial features caused by a 17q21.31 microdeletion or KANSL1 truncating variant. As the facial gestalt of KdVS has resemblance with the gestalt of the 22q11.2 deletion syndrome (22q11.2DS), we assessed whether our previously described hybrid quantitative facial phenotyping algorithm could distinguish between these two syndromes, and whether there is a facial difference between the molecular KdVS subtypes. We applied our algorithm to 2D photographs of 97 patients with KdVS (78 microdeletions, 19 truncating variants (likely) causing KdVS) and 48 patients with 22q11.2DS as well as age, gender and ethnicity matched controls with intellectual disability (n = 145). The facial gestalts of KdVS and 22q11.2DS were both recognisable through significant clustering by the hybrid model, yet different from one another (p = 7.5 × 10-10 and p = 0.0052, respectively). Furthermore, the facial gestalts of KdVS caused by a 17q21.31 microdeletion and KANSL1 truncating variant (likely) causing KdVS were indistinguishable (p = 0.981 and p = 0.130). Further application to three patients with a variant of unknown significance in KANSL1 showed that these faces do not match KdVS. Our data highlight quantitative facial phenotyping not only as a powerful tool to distinguish syndromes with overlapping facial dysmorphisms but also to establish pathogenicity of variants of unknown clinical significance.
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9
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Sixto-Costoya A, Lucas-Domínguez R, Aleixandre-Benavent R, Vidal-Infer A. Is Sharing Datasets the Answer to the New Challenges of Reproductive Biology Research? Reprod Sci 2021; 28:1023-1025. [PMID: 33594650 PMCID: PMC7886301 DOI: 10.1007/s43032-021-00484-8] [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: 09/15/2020] [Accepted: 01/31/2021] [Indexed: 10/28/2022]
Abstract
Data sharing increases the speed of research and saves time and resources while ensuring transparency and reproducibility. We have analyzed this behavior through the reproductive biology community. Our study revealed that Q1 (44%) and Q2 (36%) JCR reproductive biology journals are the most active journals in data sharing.
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Affiliation(s)
- A Sixto-Costoya
- Department of History of Science and Documentation, School of Medicine, University of Valencia, Avda. Blasco Ibañez 15, 46010, Valencia, Spain. .,UISYS, Joint Research Unit, CSIC-University of Valencia, Pza. Cisneros 4, 46003, Valencia, Spain.
| | - R Lucas-Domínguez
- Department of History of Science and Documentation, School of Medicine, University of Valencia, Avda. Blasco Ibañez 15, 46010, Valencia, Spain.,UISYS, Joint Research Unit, CSIC-University of Valencia, Pza. Cisneros 4, 46003, Valencia, Spain.,CIBERON, Valencia, Spain
| | - R Aleixandre-Benavent
- UISYS, Joint Research Unit, CSIC-University of Valencia, Pza. Cisneros 4, 46003, Valencia, Spain.,Ingenio, CSIC-Politechnic University of Valencia, Ciudad Politécnica de la Innovación, Edif 8E 4º, Camino de Vera s/n, 46022, Valencia, Spain
| | - A Vidal-Infer
- Department of History of Science and Documentation, School of Medicine, University of Valencia, Avda. Blasco Ibañez 15, 46010, Valencia, Spain.,UISYS, Joint Research Unit, CSIC-University of Valencia, Pza. Cisneros 4, 46003, Valencia, Spain
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10
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Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. JAMIA Open 2020; 3:472-486. [PMID: 33426479 PMCID: PMC7660964 DOI: 10.1093/jamiaopen/ooaa030] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/30/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.
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Affiliation(s)
- Yaffa R Rubinstein
- Special Volunteer in the Office of Strategic Initiatives, National Library of Medicine, Bethesda, Maryland, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Telethon Kids Institute, Perth, Australia
| | | | - Rebecca M Goodwin
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen C Groft
- NCATS, National Institutes of Health, Bethesda, Maryland, USA
| | - Mats G Hansson
- Center for Research Ethics and Bioethics, Uppsala Universitet, Uppsala, Sweden
| | - Nomi L Harris
- Department of Environmental Genomics & System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vojtech Huser
- Department of Health and Human Services, NCBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Deborah Mascalzoni
- Center for Research Ethics and Bioethics, Uppsala University, Sweden and EURAC Research, Bolzano, Italy
| | - Julie A McMurry
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
| | - Matthew Might
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christoffer Nellaker
- Nuffield Department of Women's and Reproductive Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dina N Paltoo
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute and Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Manuel Posada
- Rare Diseases Research Institute & CIBERER, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Marco Roos
- Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Tamar B Rubinstein
- Children Hospital at Montefiore/Albert Einstein College of Medicine—Pediatrics, Bronx, New York, USA
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Leiden, Netherlands
| | - Melissa A Haendel
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
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11
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Brunak S, Bjerre Collin C, Eva Ó Cathaoir K, Golebiewski M, Kirschner M, Kockum I, Moser H, Waltemath D. Towards standardization guidelines for in silico approaches in personalized medicine. J Integr Bioinform 2020; 17:jib-2020-0006. [PMID: 32827396 PMCID: PMC7756614 DOI: 10.1515/jib-2020-0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/26/2020] [Indexed: 01/11/2023] Open
Abstract
Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.
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Affiliation(s)
| | | | | | | | - Marc Kirschner
- University of Copenhagen, Copenhagen, Denmark
- Forschungszentrum Jülich GmbH, Project Management Jülich, Jülich, Germany
| | | | - Heike Moser
- Medical Informatics Laboratory, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Dagmar Waltemath
- Medical Informatics Laboratory, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
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12
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Michelson DJ, Clark RD. Optimizing Genetic Diagnosis of Neurodevelopmental Disorders in the Clinical Setting. Clin Lab Med 2020; 40:231-256. [PMID: 32718497 DOI: 10.1016/j.cll.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in medical genetics has changed the practice of medicine in general and child neurology in particular. A genetic diagnosis has become critically important in determining optimal management of many neurodevelopmental disorders, making genetic testing a routine consideration of patient care in outpatient and inpatient settings. Today's child neurologists should be familiar with various genetic testing modalities and their appropriate use. Molecular genetic testing of children with unexplained developmental delays and/or congenital anomalies has a 20% to 30% chance of identifying a causative etiology. Newer methods have made genetic testing more widely available and sensitive but also more likely to produce ambiguous results.
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Affiliation(s)
- David Joshua Michelson
- Division of Child Neurology, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA.
| | - Robin Dawn Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA
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13
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Bhardwaj P, Yadav RK, Kurian S. Digitizing the Pharma Neurons - A Technological Operation in Progress! Rev Recent Clin Trials 2020; 15:178-187. [PMID: 32564760 DOI: 10.2174/1574887115666200621183459] [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: 02/27/2020] [Revised: 04/27/2020] [Accepted: 05/22/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Digitization and automation are the buzzwords in clinical research and pharma companies are investigating heavily here. Right from drug discovery to personalized medicine, digital patients and patient engagement, there is great consideration of technology at each step. METHODS The published data and online information available is reviewed to give an overview of digitization in pharma, across the drug development cycle, industry collaborations and innovations. The regulatory guidelines, innovative collaborations across industry, academics and thought leadership are presented. Also included are some ideas, suggestions, way forwards while digitizing the pharma neurons, the regulatory stand, benefits and challenges. RESULTS The innovations range from discovering personalized medicine to conducting virtual clinical trials, and maximizing data collection from the real-world experience. To address the increasing demand for the real-world data and the needs of tech-savvy patients, the innovations are shaping up accordingly. Pharma companies are collaborating with academics and they are co-innovating the technology for example Massachusetts Institute of Technology's program. This focuses on the modernization of clinical trials, strategic use of artificial intelligence and machine learning using real-world evidence, assess the risk-benefit ratio of deploying digital analytics in medicine, and proactively identifying the solutions. CONCLUSION With unfolding data on the impact of science and technology amalgamation, we need shared mindset between data scientists and medical professionals to maximize the utility of enormous health and medical data. To tackle this efficiently, there is a need of cross-collaboration and education, and align with ethical and regulatory requirements. A perfect blend of industry, regulatory, and academia will ensure successful digitization of pharma neurons.
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Affiliation(s)
| | - Raj Kumar Yadav
- Integral Health Clinic, Department of Physiology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Sojan Kurian
- Tata Consultancy Services, New York, NY, United States
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