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Borg J, Loy C, Kim J, Buhagiar A, Chin C, Damle N, De Vlaminck I, Felice A, Liu T, Matei I, Meydan C, Muratani M, Mzava O, Overbey E, Ryon KA, Smith SM, Tierney BT, Trudel G, Zwart SR, Beheshti A, Mason CE, Borg J. Spatiotemporal expression and control of haemoglobin in space. Nat Commun 2024; 15:4927. [PMID: 38862545 PMCID: PMC11166948 DOI: 10.1038/s41467-024-49289-8] [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: 06/19/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
It is now widely recognised that the environment in space activates a diverse set of genes involved in regulating fundamental cellular pathways. This includes the activation of genes associated with blood homoeostasis and erythropoiesis, with a particular emphasis on those involved in globin chain production. Haemoglobin biology provides an intriguing model for studying space omics, as it has been extensively explored at multiple -omic levels, spanning DNA, RNA, and protein analyses, in both experimental and clinical contexts. In this study, we examined the developmental expression of haemoglobin over time and space using a unique suite of multi-omic datasets available on NASA GeneLab, from the NASA Twins Study, the JAXA CFE study, and the Inspiration4 mission. Our findings reveal significant variations in globin gene expression corresponding to the distinct spatiotemporal characteristics of the collected samples. This study sheds light on the dynamic nature of globin gene regulation in response to the space environment and provides valuable insights into the broader implications of space omics research.
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Affiliation(s)
- Josef Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Conor Loy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alfred Buhagiar
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Christopher Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Iwijn De Vlaminck
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alex Felice
- Department of Surgery, Faculty of Medicine and Surgery, University of Malta, Msida, MSD2080, Malta
| | - Tammy Liu
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Irina Matei
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Masafumi Muratani
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Omary Mzava
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eliah Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Scott M Smith
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Guy Trudel
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Sara R Zwart
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
- University of Texas Medical Branch, Galveston, TX, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Joseph Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta.
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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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3
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Harteveld CL, Patrinos GP, Traeger-Synodinos J, Kountouris P, Bento C, Adekile A. Submitting Novel Globin Gene Variants to Hemoglobin. Hemoglobin 2023; 47:135-136. [PMID: 37920883 DOI: 10.1080/03630269.2023.2258618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Affiliation(s)
- Cornelis L Harteveld
- Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Joanne Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, Choremeio Research Laboratory, St. Sophia's Children's Hospital, Athens, Greece
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Celeste Bento
- Department of Hematology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Adekunle Adekile
- Department of Pediatrics, Faculty of Medicine, Kuwait University
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4
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Aly NH, Elalfy MS, Elhabashy SA, Mowafy NM, Russo R, Andolfo I, Iolascon A, Ragab IA. A stepwise diagnostic approach for undiagnosed Anemia in children: A model for low-middle income country. Blood Cells Mol Dis 2023; 103:102779. [PMID: 37558589 DOI: 10.1016/j.bcmd.2023.102779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Reaching a precise diagnosis in rare inherited anemia is extremely difficult and challenging, especially in areas with limited use of genetic studies, which makes undiagnosed anemia a unique clinical entity in tertiary hematology centers. In this study, we aim at plotting a stepwise diagnostic approach in children with undiagnosed anemia while identifying indications for genetic testing. PATIENTS AND METHODS A one-year cross-sectional study involved 44 children and adolescents with undiagnosed anemia after undergoing an initial routine panel of investigations. They were classified based on mean corpuscular volume (MCV) into 3 groups: microcytic (n = 19), normocytic (n = 14) and macrocytic (n = 11). An algorithm that included four levels of investigations was devised for each category. RESULTS After applying a systematic diagnostic approach, 33 patients (75 %) were diagnosed of whom 7 (15 %) had combined diagnoses, while 11 (25 %) patients remained undiagnosed. Based on the first, second, third and fourth levels of investigations, patients were diagnosed, respectively, as follows: of the 11 patients, 7 were microcytic, 3 normocytic and 1 macrocytic; of the 7 patients, 2 were microcytic, 2 normocytic, and 3 macrocytic; of 10 patients, 5 were microcytic, 4 normocytic and 1 macrocytic; finally, of the 16 patients, 8 were microcytic, 6 normocytic and 2 macrocytic. Numbers recorded appear higher than the actual number of the patients because some of them were diagnosed by more than one level of investigation. The diagnoses obtained in the microcytic group showed hemoglobinopathies, iron refractory iron deficiency anemia (IRIDA), membrane defects, sideroblastic anemia, hypo-transferrinemia, a combined diagnosis of sickle cell trait and pyropoikilocytosis. The diagnoses also showed a combined diagnosis of hereditary spherocytosis (HS) and alpha thalassemia minor, and a combined diagnosis of iron deficiency anemia and beta thalassemia minor, while 15 % remained undiagnosed. In the normocytic group, the diagnosis revealed autosomal recessive (AR) HS, vitamin B12 deficiency, pyruvate kinase deficiency (PKD), congenital dyserythropoietic anemia (CDA) type I, Diamond Blackfan anemia and beta thalassemia major. In addition, it showed a combined diagnosis of AR HS and CDA type II, a combined diagnosis of AR HS and PKD, and a combined diagnosis of dehydrated stomatocytosis (DHS) and G6PD carrier, meanwhile 20 % remained undiagnosed. Finally, the macrocytic group was diagnosed by vitamin B12 deficiency, sideroblastic anemia, PKD, a combined diagnosis of PKD and G6PD deficiency carrier, while 45 % remained undiagnosed. CONCLUSION Conducting a stepwise approach with different levels of investigations may help reach the diagnosis of difficult anemia without having to resort to unnecessary investigations. Combined diagnosis is an important cause of undiagnosed anemia, especially in countries with high frequency of consanguinity. The remaining 25 % of the patients continued to be undiagnosed, requiring more sophisticated investigations.
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Affiliation(s)
- Nihal Hussien Aly
- Department of Pediatrics, Hematology-Oncology Unit, Ain Shams University, Faculty of Medicine, Cairo, Egypt.
| | - Mohsen Saleh Elalfy
- Department of Pediatrics, Hematology-Oncology Unit, Ain Shams University, Faculty of Medicine, Cairo, Egypt
| | - Safinaz Adel Elhabashy
- Department of Pediatrics, Hematology-Oncology Unit, Ain Shams University, Faculty of Medicine, Cairo, Egypt
| | - Nadia Mohamed Mowafy
- Department of Clinical pathology, Ain Shams University, Faculty of Medicine, Cairo, Egypt
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy; CEINGE Biotecnologie Avanzate, Franco, Salvatore
| | - Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy; CEINGE Biotecnologie Avanzate, Franco, Salvatore
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy; CEINGE Biotecnologie Avanzate, Franco, Salvatore
| | - Iman Ahmed Ragab
- Department of Pediatrics, Hematology-Oncology Unit, Ain Shams University, Faculty of Medicine, Cairo, Egypt; Ibn Sina National College, Jeddah, KSA
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5
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Reichardt JKV, Patrinos GP, Lai PS, Novelli G. J'Accuse….. Or The Plight of pro-bono Volunteer Scientists in Academic Publishing. Hum Genomics 2022; 16:44. [PMID: 36171619 PMCID: PMC9516807 DOI: 10.1186/s40246-022-00413-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
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6
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Harteveld CL, Achour A, Arkesteijn SJG, Ter Huurne J, Verschuren M, Bhagwandien-Bisoen S, Schaap R, Vijfhuizen L, El Idrissi H, Koopmann TT. The hemoglobinopathies, molecular disease mechanisms and diagnostics. Int J Lab Hematol 2022; 44 Suppl 1:28-36. [PMID: 36074711 PMCID: PMC9542123 DOI: 10.1111/ijlh.13885] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
Hemoglobinopathies are the most common monogenic disorders in the world with an ever increasing global disease burden each year. As most hemoglobinopathies show recessive inheritance carriers are usually clinically silent. Programmes for preconception and antenatal carrier screening, with the option of prenatal diagnosis are considered beneficial in many endemic countries. With the development of genetic tools such as Array analysis and Next Generation Sequencing in addition to state of the art screening at the hematologic, biochemic and genetic level, have contributed to the discovery of an increasing number of rare rearrangements and novel factors influencing the disease severity over the recent years. This review summarizes the basic requirements for adequate carrier screening analysis, the importance of genotype–phenotype correlation and how this may lead to the unrevealing exceptional interactions causing a clinically more severe phenotype in otherwise asymptomatic carriers. A special group of patients are β‐thalassemia carriers presenting with features of β‐thalassemia intermedia of various clinical severity. The disease mechanisms may involve duplicated α‐globin genes, mosaic partial Uniparental Isodisomy of chromosome 11p15.4 where the HBB gene is located or haplo‐insufficiency of a non‐linked gene SUPT5H on chromosome 19q, first described in two Dutch families with β‐thalassemia trait without variants in the HBB gene.
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Affiliation(s)
- Cornelis L Harteveld
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Ahlem Achour
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands.,Department of congenital and hereditary diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sandra J G Arkesteijn
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeanet Ter Huurne
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike Verschuren
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Rianne Schaap
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Linda Vijfhuizen
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Hakima El Idrissi
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
| | - Tamara T Koopmann
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, The Netherlands
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7
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NGS4THAL, a one-stop molecular diagnosis and carrier screening tool for thalassemia and other hemoglobinopathies by next-generation sequencing. J Mol Diagn 2022; 24:1089-1099. [PMID: 35868510 DOI: 10.1016/j.jmoldx.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 04/03/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
Thalassemia is one of the most common genetic diseases and a major health threat worldwide. Accurate, efficient and scalable analysis of next-generation sequencing (NGS) data is much needed for its molecular diagnosis and carrier screening. We developed NGS4THAL, a bioinformatics analysis pipeline analyzing next generation sequencing (NGS) data to detect pathogenic variants for thalassemia and other hemoglobinopathies. NGS4THAL realigns ambiguously mapped NGS reads derived from the homologous hemoglobin gene clusters for accurate detection of point mutations and small insertion/deletions (InDels). It uses a combination of complementary structural variant (SV) detection tools and an inhouse database of control data containing specific SVs to achieve accurate detection of the complex SV types. Detected variants are matched with those in HbVar database, allowing recognition of known pathogenic variants, including disease modifiers. Tested on simulation data, NGS4THAL achieved high sensitivity and specificity. For targeted NGS sequencing data from samples with laboratory-confirmed pathogenic hemoglobin variants, it achieved 100% detection accuracy. Application of NGS4THAL on whole genome sequencing data from unrelated studies revealed thalassemia mutation carrier rates for Hong Kong Chinese and Northern Vietnamese that were consistent with previous reports. NGS4THAL is a highly accurate and efficient molecular diagnosis tool for thalassemia and other hemoglobinopathies based on tailored analysis of NGS data and is potentially scalable for population carrier screening.
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8
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Prime Editor 3 Mediated Beta-Thalassemia Mutations of the HBB Gene in Human Erythroid Progenitor Cells. Int J Mol Sci 2022; 23:ijms23095002. [PMID: 35563395 PMCID: PMC9099916 DOI: 10.3390/ijms23095002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Recently developed Prime Editor 3 (PE3) has been implemented to induce genome editing in various cell types but has not been proven in human hematopoietic stem and progenitor cells. Using PE3, we successfully installed the beta-thalassemia (beta-thal) mutations in the HBB gene in the erythroid progenitor cell line HUDEP-2. We inserted the mCherry reporter gene cassette into editing plasmids, each including the prime editing guide RNA (pegRNA) and nick sgRNA. The plasmids were electroporated into HUDEP-2 cells, and the PE3 modified cells were identified by mCherry expression and collected using fluorescence-activated cell sorting (FACS). Sanger sequencing of the positive cells confirmed that PE3 induced precise beta-thal mutations with editing ratios from 4.55 to 100%. Furthermore, an off-target analysis showed no unintentional edits occurred in the cells. The editing ratios and parameters of pegRNA and nick sgRNA were also analyzed and summarized and will contribute to enhanced PE3 design in future studies. The characterization of the HUDEP-2 beta-thal cells showed typical thalassemia phenotypes, involving ineffective erythropoiesis, abnormal erythroid differentiation, high apoptosis rate, defective alpha-globin colocalization, cell viability deterioration, and ROS resisting deficiency. These HUDEP-2 beta-thal cells could provide ideal models for future beta-thal gene therapy studies.
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9
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Chauhan W, Shoaib S, Fatma R, Zaka‐ur‐Rab Z, Afzal M. β‐thalassemia, and the advent of new Interventions beyond Transfusion and Iron chelation. Br J Clin Pharmacol 2022; 88:3610-3626. [DOI: 10.1111/bcp.15343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 01/19/2023] Open
Affiliation(s)
- Waseem Chauhan
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
| | - Shoaib Shoaib
- Department of Biochemistry, JNMC Aligarh Muslim University Aligarh India
| | - Rafat Fatma
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
| | - Zeeba Zaka‐ur‐Rab
- Department of Pediatrics, JNMC Aligarh Muslim University Aligarh India
| | - Mohammad Afzal
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
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10
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Wang XX, Ma YY, Zhang W, Liu JY, Su LY, Su H, Lin XY, Yuan JY, Wang Y, Liu YC, Lai MM. Prevalence and Genetic Analysis of β-Thalassemia in the Dali Bai Autonomous Prefecture of the Yunnan Province, China. Genet Test Mol Biomarkers 2022; 26:152-156. [PMID: 35349373 DOI: 10.1089/gtmb.2021.0242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiao-xuan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Dali University, Dali, China
| | - Yu-yuan Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Dali University, Dali, China
| | - Wei Zhang
- Guangzhou Kingmed Diagnostics Group Co., Ltd., Guangzhou, China
| | - Jia-yao Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Dali University, Dali, China
| | - Lan-ying Su
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, Dali, China
| | - Hui Su
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, Dali, China
| | - Xiao-yan Lin
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, Dali, China
| | - Jin-ying Yuan
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, Dali, China
| | - Yan Wang
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, Dali, China
| | - Yun-chun Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Dali University, Dali, China
| | - Ming-ming Lai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Dali University, Dali, China
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11
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Xian J, Wang Y, He J, Li S, He W, Ma X, Li Q. Molecular Epidemiology and Hematologic Characterization of Thalassemia in Guangdong Province, Southern China. Clin Appl Thromb Hemost 2022; 28:10760296221119807. [PMID: 35979587 PMCID: PMC9393661 DOI: 10.1177/10760296221119807] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Introduction: About 2% of the population in the world are carriers
of the thalassemia gene. Thalassemia is highly prevalent in Southern China, and
traditional clinical testing methods would cause missed diagnosis of partial
static thalassemia. Here, we reviewed and summarized a set of simple and
clinically feasible thalassemia detection protocols adopted by the Prenatal
Diagnosis and Reproductive Center of our hospital. Methods: From
January 1, 2015, to December 31, 2020, 31 512 peripheral blood samples and 3828
prenatal samples were collected in our study. All the peripheral blood samples
were performed through thalassemia screening by routine blood tests and
hemoglobin electrophoresis and gene detection. The prenatal diagnosis would be
implemented for the fetus if the parents were carriers of the same type of
thalassemia. Results: A total of 6137 (19.48%) cases were diagnosed
as thalassemia, in which 4749 (15.07%) were α-thalassemia, 1196 (3.80%) were
β-thalassemia and 192 (0.61%) were co-inheritance of α- and β-thalassemia. For
prenatal samples, 3160 (82.55%) cases were diagnosed as thalassemia, in which
2021 (52.80%) were α-thalassemia, 997 (26.05%) were β-thalassemia and 142
(3.71%) were co-inheritance of α- and β-thalassemia. In addition, we also found
five novel mutations, including NC_000016.9:g.223681-227492del3812; HBA1:
c.301-31_301-24delCTCGGCCCinsG; HBA2: c.95+7C>T for α-thalassemia and HBB:
c.263_276delCACTGAGTGAGCTG; HBB: c.315+143G>A for β-thalassemia.
Conclusion: The present study updates the epidemiological
characteristics and mutation spectrum of thalassemia in Southern China and
demonstrated five novel mutations. Our research provides a reference for
clinical diagnosis and treatment, prenatal diagnosis, or reproductive genetic
counseling for patients with thalassemia in Guangdong.
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Affiliation(s)
- Jiajia Xian
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Yanchao Wang
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Jianchun He
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Shaoying Li
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Wenzhi He
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Xiaoyan Ma
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Qing Li
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, 117980The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
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12
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Forero DA, Curioso WH, Patrinos GP. The importance of adherence to international standards for depositing open data in public repositories. BMC Res Notes 2021; 14:405. [PMID: 34727971 PMCID: PMC8561348 DOI: 10.1186/s13104-021-05817-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
There has been an important global interest in Open Science, which include open data and methods, in addition to open access publications. It has been proposed that public availability of raw data increases the value and the possibility of confirmation of scientific findings, in addition to the potential of reducing research waste. Availability of raw data in open repositories facilitates the adequate development of meta-analysis and the cumulative evaluation of evidence for specific topics. In this commentary, we discuss key elements about data sharing in open repositories and we invite researchers around the world to deposit their data in them.
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Affiliation(s)
- Diego A Forero
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia. .,Professional Program in Respiratory Therapy, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia.
| | - Walter H Curioso
- Vicerrectorado de Investigación, Universidad Continental, Lima, Peru
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, UAE
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13
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Patrinos GP, Chui DHK, Hardison RC, Steinberg MH. Strategies to improve pharmacogenomic-guided treatment options for patients with β-hemoglobinopathies. Expert Rev Hematol 2021; 14:883-885. [PMID: 34490838 PMCID: PMC9306350 DOI: 10.1080/17474086.2021.1977117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Drug efficacy and toxicity are closely related to the unique genetic profile of individuals, or pharmacogenomics. Despite the fact that cardiology, psychiatry and oncology are among the clinical specialties in which pharmacogenomics has become a clinical reality, the utility of pharmacogenomics has yet to be demonstrated for several other medical specialties. Over the last 15 years, genomic variants in a number of loci have been shown to be significantly associated with the fetal hemoglobin (HbF) response to hydroxyurea, the only approved drug for HbF induction for sickle cell disease. Here, we provide an update and discuss future challenges to the application of pharmacogenomics to improve therapies for β-hemoglobinopathies in relation to the current pharmacological treatment modalities for those disorders.
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Affiliation(s)
- George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece
- United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, UAE
- United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
| | - David H. K. Chui
- Boston University School of Medicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
| | - Ross C. Hardison
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, PA, USA
| | - Martin H. Steinberg
- Boston University School of Medicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
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14
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Shen Y, Verboon JM, Zhang Y, Liu N, Kim YJ, Marglous S, Nandakumar SK, Voit RA, Fiorini C, Ejaz A, Basak A, Orkin SH, Xu J, Sankaran VG. A unified model of human hemoglobin switching through single-cell genome editing. Nat Commun 2021; 12:4991. [PMID: 34404810 PMCID: PMC8371164 DOI: 10.1038/s41467-021-25298-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Key mechanisms of fetal hemoglobin (HbF) regulation and switching have been elucidated through studies of human genetic variation, including mutations in the HBG1/2 promoters, deletions in the β-globin locus, and variation impacting BCL11A. While this has led to substantial insights, there has not been a unified understanding of how these distinct genetically-nominated elements, as well as other key transcription factors such as ZBTB7A, collectively interact to regulate HbF. A key limitation has been the inability to model specific genetic changes in primary isogenic human hematopoietic cells to uncover how each of these act individually and in aggregate. Here, we describe a single-cell genome editing functional assay that enables specific mutations to be recapitulated individually and in combination, providing insights into how multiple mutation-harboring functional elements collectively contribute to HbF expression. In conjunction with quantitative modeling and chromatin capture analyses, we illustrate how these genetic findings enable a comprehensive understanding of how distinct regulatory mechanisms can synergistically modulate HbF expression. Genetic mechanisms underlying fetal hemoglobin (HbF) regulation and switching are not fully understood. Here, the authors develop a single-cell genome editing functional assay to model how effects of mutation-harbouring functional elements contribute to HbF expression.
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Affiliation(s)
- Yong Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nan Liu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samantha Marglous
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ayesha Ejaz
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anindita Basak
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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15
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Du L, Bao X, Qin D, Wang J, Yao C, Liang J, Chen J, Yin A. Compounded with hemoglobin Port Phillip and -α 4.2 or -- SEA deletions were identified in Chinese population. Mol Genet Genomic Med 2021; 9:e1699. [PMID: 34398528 PMCID: PMC8457688 DOI: 10.1002/mgg3.1699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Introduction Although over 1000 hemoglobin (Hb) variants were identified so far, Hb Port Phillip compound with α‐thalassemia deletion had no reported before. Methods Two patients and the associated families from Guangdong province in China were recruited. Hematological parameters were determined by blood routine examination and hemoglobin electrophoresis. Genotyping was performed by Gap‐PCR and Sanger sequencing. Results One patient was diagnosed as Hb Port Phillip, while her daughter was compounded with ‐α4.2 deletion, with normal Hb level (150 g/L), mean corpuscular volume (MCV) 108.4 fl and mean corpuscular hemoglobin (MCH) (30.5 pg). Another patient was diagnosed as compound Hb Port Phillip and ‐‐SEA deletion. This proband presented with more severe α‐thalassemia trait than the patient compounded with ‐α4.2 deletion, with hemoglobin 80 g/L, MCV 61.7 fl, and MCH 18.7 pg. Conclusion Here we first time identified two patients compound with Hb Port Phillip and ‐α4.2 and ‐‐SEA deletions, respectively, which had never been reported. Our study widens the genotypes of hemoglobinopathy and provides reference for genetic counselling and prenatal diagnosis in this population.
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Affiliation(s)
- Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Xiuqin Bao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Danqing Qin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Jicheng Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Cuize Yao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Jie Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
| | - Jianhong Chen
- Prenatal Diagnosis Center, Huizhou No.1 Maternal and Child Care Service Center, Huizhou, China
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.,Guangdong Birth Defect Prevention and Management Center, Guangzhou, Guangdong, China
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16
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Kasmi C, Amri Y, Hadj-Fredj S, Oueslati S, Dabboussi M, Mahjoub R, Hammami S, Aljane I, Mami FB, Jamoussi H, Messaoud T, Bibi A. Analysis of δ-globin gene alleles in Tunisians: description of three new delta-thalassemia mutations. Mol Biol Rep 2021; 48:5923-5933. [PMID: 34341901 DOI: 10.1007/s11033-021-06592-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/23/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Thalassemia is one of the most prevalent worldwide autosomal recessive disorders characterized by a great molecular and clinical expression heterogeneity. Alpha and beta-thalassemia are the main two types observed in case of mutations affecting alpha and beta-globin genes respectively. Delta-thalassemia is noted when mutations occur on the delta-globin gene. In Tunisia, β-thalassemia prevalence is estimated at 2.21% of carriers. However, few reports investigated the delta-globin gene. OBJECTIVES In this work, we aimed to perform a molecular study to help define the molecular spectrum of δ-thalassemia mutations in Tunisia. PATIENTS AND METHODS The study involved 7558 patients among whom we selected 179 individuals with abnormal HbA2 values or fractions. Hemoglobin analysis was performed using Capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC). DNA sequencing was performed on ABI prism 310 Genetic Analyzer Applied Biosystems. CUPSAT (Cologne University Protein Stability Analysis Tool) was used for the prediction of protein stability changes upon missense mutations and mutants were modeled via DeepView-SwissPdbViewer and POV-Ray softwares for molecular dynamics simulation studies. RESULTS We identified four mutations: HbA2-Yialousa described for the first time in Tunisia ( in 72.72% of cases) and 3 mutations reported for the first time in the world: (i) c.442 T > C Stop147Arg ext 15aa-stop observed in 18.18% of cases, (ii) c.187 G > C (Ala62Pro) noted in 4.54% of cases and (iii) c.93-1G > C found in 4.54% of cases. CONCLUSION Our data provide genetic basis that would be especially useful in screening for beta-thalassemia trait during delta-beta thalassemia associations.
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Affiliation(s)
- Chaima Kasmi
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia.
| | - Yessine Amri
- Laboratory of Biochemistry and Molecular Biology, Research Laboratory LR00SP03, BéchirHamza Children's Hospital, Tunis, Tunisia
| | - Sondess Hadj-Fredj
- Laboratory of Biochemistry and Molecular Biology, Research Laboratory LR00SP03, BéchirHamza Children's Hospital, Tunis, Tunisia
| | - Sabrine Oueslati
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Malek Dabboussi
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Rahma Mahjoub
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Sana Hammami
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Imen Aljane
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Faika Ben Mami
- Department of Nutritional Diseases C, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Henda Jamoussi
- Obesity Research Unit, Department of Nutritional Diseases A, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Taieb Messaoud
- Laboratory of Biochemistry and Molecular Biology, Research Laboratory LR00SP03, BéchirHamza Children's Hospital, Tunis, Tunisia
| | - Amina Bibi
- Research Unit UR17SP01Laboratory of Clinical Biology, Molecular Biology Applied To the Study of Hyperlipoproteinemias, Diabetes and Hormones, National Institute of Nutrition and Food Technology, 11 Street Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
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17
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Hottentot QP, de Meijer E, Buermans HPJ, White SJ, Harteveld CL. Breakpoint characterization of a rare alpha 0 -thalassemia deletion using targeted locus amplification on genomic DNA. Int J Lab Hematol 2021; 43:1628-1634. [PMID: 34251753 PMCID: PMC9291876 DOI: 10.1111/ijlh.13651] [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: 04/02/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Introduction The high‐sequence homology of the α‐globin‐gene cluster is responsible for microhomology‐mediated recombination events during meiosis, resulting in a high density of deletion breakpoints within a 10 kb region. Commonly used deletion detection methods, such as multiplex ligation‐dependent probe amplification (MLPA) and Southern blot, cannot exactly define the breakpoints. This typically requires long‐range PCR, which is not always successful. Targeted locus amplification (TLA) is a targeted enrichment method that can be used to sequence up to 70 kb of neighboring DNA sequences without prior knowledge about the target site. Methods Genomic DNA (gDNA) TLA is a technique that folds isolated DNA, ensuring that adjacent loci are in a close spatial proximity. Subsequent digestion and religation form DNA circles that are amplified using fragment‐specific inverse primers, creating a library that is suitable for Illumina sequencing. Results Here, we describe the characterization of a rare 16 771 bp deletion, utilizing gDNA TLA with a single inverse PCR primer set on one end of the breakpoint. Primers for breakpoint PCR were designed to confirm the deletion breakpoints and were consequently used to characterize the same deletion in 10 additional carriers sharing comparable hematologic data and similar MLPA results. Conclusions The gDNA TLA technology was successfully used to identify deletion breakpoints within the alpha‐globin cluster. The deletion was described only once in an earlier study as the ‐‐gb, but as it was not registered correctly in the available databases, it was not initially recognized as such.
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Affiliation(s)
- Quint P Hottentot
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Emile de Meijer
- Leiden Genome Technology Centre, Leiden University Medical Centre, Leiden, the Netherlands
| | - Henk P J Buermans
- Leiden Genome Technology Centre, Leiden University Medical Centre, Leiden, the Netherlands
| | - Stefan J White
- Leiden Genome Technology Centre, Leiden University Medical Centre, Leiden, the Netherlands
| | - Cornelis L Harteveld
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
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18
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Karamperis K, Tsoumpeli MT, Kounelis F, Koromina M, Mitropoulou C, Moutinho C, Patrinos GP. Genome-based therapeutic interventions for β-type hemoglobinopathies. Hum Genomics 2021; 15:32. [PMID: 34090531 PMCID: PMC8178887 DOI: 10.1186/s40246-021-00329-0] [Citation(s) in RCA: 4] [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: 02/06/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022] Open
Abstract
For decades, various strategies have been proposed to solve the enigma of hemoglobinopathies, especially severe cases. However, most of them seem to be lagging in terms of effectiveness and safety. So far, the most prevalent and promising treatment options for patients with β-types hemoglobinopathies, among others, predominantly include drug treatment and gene therapy. Despite the significant improvements of such interventions to the patient's quality of life, a variable response has been demonstrated among different groups of patients and populations. This is essentially due to the complexity of the disease and other genetic factors. In recent years, a more in-depth understanding of the molecular basis of the β-type hemoglobinopathies has led to significant upgrades to the current technologies, as well as the addition of new ones attempting to elucidate these barriers. Therefore, the purpose of this article is to shed light on pharmacogenomics, gene addition, and genome editing technologies, and consequently, their potential use as direct and indirect genome-based interventions, in different strategies, referring to drug and gene therapy. Furthermore, all the latest progress, updates, and scientific achievements for patients with β-type hemoglobinopathies will be described in detail.
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Affiliation(s)
- Kariofyllis Karamperis
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
- The Golden Helix Foundation, London, UK
| | - Maria T Tsoumpeli
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Fotios Kounelis
- Department of Computing, Group of Large-Scale Data & Systems, Imperial College London, London, UK
| | - Maria Koromina
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
| | | | - Catia Moutinho
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece.
- College of Medicine and Health Sciences, Department of Pathology, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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19
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Giardine BM, Joly P, Pissard S, Wajcman H, K Chui DH, Hardison RC, Patrinos GP. Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res 2021; 49:D1192-D1196. [PMID: 33125055 PMCID: PMC7778921 DOI: 10.1093/nar/gkaa959] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is a widely-used locus-specific database (LSDB) launched 20 years ago by a multi-center academic effort to provide timely information on the numerous genomic variants leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Here, we report several advances for the database. We made clinically relevant updates of HbVar, implemented as additional querying options in the HbVar query page, allowing the user to explore the clinical phenotype of compound heterozygous patients. We also made significant improvements to the HbVar front page, making comparative data querying, analysis and output more user-friendly. We continued to expand and enrich the regular data content, involving 1820 variants, 230 of which are new entries. We also increased the querying potential and expanded the usefulness of HbVar database in the clinical setting. These several additions, expansions and updates should improve the utility of HbVar both for the globin research community and in a clinical setting.
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Affiliation(s)
- Belinda M Giardine
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA
| | - Philippe Joly
- Biochimie des pathologies érythrocytaires, Laboratoire de Biochimie et Biologie Moléculaire Grand-Est, Groupement hospitalier Est, Hospices Civils de Lyon, Bron, France.,Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge'', Université Claude Bernard Lyon 1, COMUE Lyon, France
| | - Serge Pissard
- Assistance Publique Hopitaux de Paris), Department of Genetics GHU (Groupe Hospitalier Universitaire Henri Mondor) H. Mondor and Institut Mondor de Recherche biomedicale - INSERM U955 eq2, Creteil France
| | | | - David H K Chui
- Boston University School of Medicine, Department of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
| | - Ross C Hardison
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece.,Erasmus University Medical Center Rotterdam, Faculty of Medicine and Health Sciences, Department of Pathology, Bioinformatics Unit, Rotterdam, the Netherlands.,United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, UAE.,United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
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20
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Rahmani S, Ansarihadipour H, Bayatiani MR, Khosrowbeygi A, Babaei S, Rasmi Y. Conformational changes of β-thalassemia major hemoglobin and oxidative status of plasma after in vitro exposure to extremely low-frequency electromagnetic fields: An artificial neural network analysis. Electromagn Biol Med 2021; 40:117-130. [PMID: 33092422 DOI: 10.1080/15368378.2020.1830289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
Electromagnetic fields (EMF) can generate reactive oxygen species and induce oxidative modifications. We investigated the effects of extremely low-frequency electromagnetic fields (ELF-EMF) on oxidative status of plasma and erythrocytes in β-thalassemia major patients and design artificial neural networks (ANN) for evaluating the oxyHb concentration. Blood samples were obtained from age and sex-matched healthy donors (n = 12) and major β-thalassemia patients (n = 12) and subjected to 0.5 and 1 mT and 50 Hz of EMF. Plasma oxidative status was estimated after 1 and 2 h exposure to ELE-EMF. Structural changes of plasma proteins were investigated by Native PAGE and SDS-PAGE. Moreover; multilayer perceptron (MLP) method was applied for designing a feed forward ANN model to predict the impact of these oxidative and antioxidative parameters on oxyHb concentration. Two hour exposure to ELF-EMF induced significant oxidative changes on major β-thalassemia samplesElectrophoretic profiles showed two high molecular weight (HMW) protein aggregates in plasma samples from healthy donors and major β-thalassemia patients. According to our ANN design, the main predictors of oxyHb concentration were optical density of Hb at 542, 340, 569, 630, 577, and 420 nm and metHb and hemichrome (HC) concentration. Accuracy of the proposed ANN model was shown by predicted by observed chart (y = 1.3 + 0.96x, R2 = 0.942), sum of squares errors (SSR), and relative errors (RE). Our results showed the detailed effects of ELF-EMF on Hb structure and oxidative balance of plasma in major β-thalassemia patients and significance of ANN analysis during normal and pathologic conditions.
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Affiliation(s)
- Saeideh Rahmani
- Department of Biochemistry and Genetics, School of Medicine, Arak University of Medical Sciences , Arak, Iran
| | - Hadi Ansarihadipour
- Department of Biochemistry and Genetics, School of Medicine, Arak University of Medical Sciences , Arak, Iran
| | - Mohamad Reza Bayatiani
- Department of Medical Physics and Radiotherapy, Arak University of Medical Sciences and Khansari Hospital , Arak, Iran
| | - Ali Khosrowbeygi
- Department of Biochemistry and Genetics, School of Medicine, Arak University of Medical Sciences , Arak, Iran
| | - Saeid Babaei
- Department of Anatomical Sciences, School of Medicine, Arak University of Medical Sciences , Arak, Iran
| | - Yousef Rasmi
- Department of Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences , Urmia, Iran
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21
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Abstract
Over a thousand diseases are caused by mutations that alter gene expression levels. The potential of nuclease-deficient zinc fingers, TALEs or CRISPR fusion systems to treat these diseases by modulating gene expression has recently emerged. These systems can be applied to modify the activity of gene-regulatory elements - promoters, enhancers, silencers and insulators, subsequently changing their target gene expression levels to achieve therapeutic benefits - an approach termed cis-regulation therapy (CRT). Here, we review emerging CRT technologies and assess their therapeutic potential for treating a wide range of diseases caused by abnormal gene dosage. The challenges facing the translation of CRT into the clinic are discussed.
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22
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Patrinos GP, Pasparakis E, Koiliari E, Pereira AC, Hünemeier T, Pereira LV, Mitropoulou C. Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries. Am J Hum Genet 2020; 107:589-595. [PMID: 33007198 DOI: 10.1016/j.ajhg.2020.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.
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23
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Kalle Kwaifa I, Lai MI, Md Noor S. Non-deletional alpha thalassaemia: a review. Orphanet J Rare Dis 2020; 15:166. [PMID: 32600445 PMCID: PMC7322920 DOI: 10.1186/s13023-020-01429-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Defective synthesis of the α-globin chain due to mutations in the alpha-globin genes and/or its regulatory elements leads to alpha thalassaemia syndrome. Complete deletion of the 4 alpha-globin genes results in the most severe phenotype known as haemoglobin Bart's, which leads to intrauterine death. The presence of one functional alpha gene is associated with haemoglobin H disease, characterised by non-transfusion-dependent thalassaemia phenotype, while silent and carrier traits are mostly asymptomatic. MAIN BODY Clinical manifestations of non-deletional in alpha thalassaemia are varied and have more severe phenotype compared to deletional forms of alpha thalassaemia. Literature for the molecular mechanisms of common non-deletional alpha thalassaemia including therapeutic measures that are necessarily needed for the understanding of these disorders is still in demand. This manuscript would contribute to the better knowledge of how defective production of the α-globin chains due to mutations on the alpha-globin genes and/or the regulatory elements leads to alpha thalassaemia syndrome. CONCLUSION Since many molecular markers are associated with the globin gene expression and switching over during the developmental stages, there is a need for increased awareness, new-born and prenatal screening program, especially for countries with high migration impact, and for improving the monitoring of patients with α-thalassaemia.
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Affiliation(s)
- Ibrahim Kalle Kwaifa
- Haematology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Department of Haematology, School of Medical Laboratory Sciences, College of Health Sciences, Usmanu Danfodiyo University (UDU), Sokoto, North-Western, Nigeria
| | - Mei I Lai
- Haematology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia(UPM), Serdang, Selangor, Malaysia
| | - Sabariah Md Noor
- Haematology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia (UPM), Serdang, Selangor, Malaysia.
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24
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Kounelis F, Kanterakis A, Kanavos A, Pandi MT, Kordou Z, Manusama O, Vonitsanos G, Katsila T, Tsermpini EE, Lauschke VM, Koromina M, van der Spek PJ, Patrinos GP. Documentation of clinically relevant genomic biomarker allele frequencies in the next-generation FINDbase worldwide database. Hum Mutat 2020; 41:1112-1122. [PMID: 32248568 DOI: 10.1002/humu.24018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/25/2020] [Accepted: 03/22/2020] [Indexed: 01/24/2023]
Abstract
FINDbase (http://www.findbase.org) is a comprehensive data resource recording the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants underlying genetic disorders as well as pharmacogenomic biomarkers that can guide drug treatment. Here, we report significant new developments and technological advancements in the database architecture, leading to a completely revamped database structure, querying interface, accompanied with substantial extensions of data content and curation. In particular, the FINDbase upgrade further improves the user experience by introducing responsive features that support a wide variety of mobile and stationary devices, while enhancing computational runtime due to the use of a modern Javascript framework such as ReactJS. Data collection is significantly enriched, with the data records being divided in a Public and Private version, the latter being accessed on the basis of data contribution, according to the microattribution approach, while the front end was redesigned to support the new functionalities and querying tools. The abovementioned updates further enhance the impact of FINDbase, improve the overall user experience, facilitate further data sharing by microattribution, and strengthen the role of FINDbase as a key resource for personalized medicine applications and personalized public health.
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Affiliation(s)
- Fotios Kounelis
- Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, Patras, Greece
| | - Alexandros Kanterakis
- Biomedical Informatics Laboratory, Foundation of Research and Technology Hellas, Heraklion, Greece.,Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Andreas Kanavos
- Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, Patras, Greece.,Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Maria-Theodora Pandi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Bioinformatics Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Medical Center, Erasmus University, Rotterdam, The Netherlands
| | - Zoe Kordou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Olivia Manusama
- Department of Immunology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gerasimos Vonitsanos
- Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, Patras, Greece.,Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Koromina
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Peter J van der Spek
- Bioinformatics Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Medical Center, Erasmus University, Rotterdam, The Netherlands
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Bioinformatics Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Medical Center, Erasmus University, Rotterdam, The Netherlands.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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25
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Zhao J, Li J, Lai Q, Yu Y. Combined use of gap-PCR and next-generation sequencing improves thalassaemia carrier screening among premarital adults in China. J Clin Pathol 2020; 73:488-492. [PMID: 31980563 PMCID: PMC7398480 DOI: 10.1136/jclinpath-2019-206339] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022]
Abstract
Aims Thalassaemia is one of the most common genetics disorders in the world, especially in southern China. The aim of the present study was to investigate the feasibility of combining the gap-PCR and next-generation sequencing (NGS) for thalassaemia carrier screening in the Chinese population. Methods Blood samples were obtained from 944 prepregnancy couples; thalassaemia carrier screening was performed by using a routine haematological method and a combination of gap-PCR and NGS method. Results We found that the α thalassaemia carrier rate was 11% (207/1888); the β thalassaemia carrier rate was 3.7% (70/1888); the composite α thalassaemia and β thalassaemia carrier rate was 0.4% (8/1888). We also identified seven novel mutations, including HBA1: c.412A>G, −50 (G>A), HBB: c.*+129T>A, HBB: c.-64G>C, HBB: c.-180G>C, HBB: c.*+5G>A and HBB: c.-113A>G. By comparing the combined gap-PCR and NGS method, the MCV+MCH and HbA2 detection strategy showed a lower sensitivity of 61.05% (105/172) and a higher missed diagnosis ratio of 38.95% (67/172) for α thalassaemia mutations. The sensitivity was improved with the MCV+MCH and HbA2 detection screen when compared with MCV+MCH detection for β thalassaemia (98.51% vs 85.90%). Conclusions Our study suggests the combined gap-PCR and NGS method is a cost-effective method for the thalassaemia carrier screening, particularly for the α thalassaemia mutation carriers.
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Affiliation(s)
- Jianghong Zhao
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
| | - Jia Li
- Department of Thyroid and Breast, Shanghai Tenth People's Hospital, Shanghai, China
| | - Qiaohong Lai
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
| | - Yanping Yu
- Department of Obstetrics and Gynecology, Xiaolan Hospital Affiliated to Southern Medical University, Zhongshan, Guangdong province, China
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26
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Zhang L, Zhang Q, Tang Y, Cong P, Ye Y, Chen S, Zhang X, Chen Y, Zhu B, Cai W, Chen S, Cai R, Guo X, Zhang C, Zhou Y, Zou J, Liu Y, Chen B, Yan S, Chen Y, Zhou Y, Ding H, Li X, Chen D, Zhong J, Shang X, Liu X, Qi M, Xu X. LOVD-DASH: A comprehensive LOVD database coupled with diagnosis and an at-risk assessment system for hemoglobinopathies. Hum Mutat 2019; 40:2221-2229. [PMID: 31286593 PMCID: PMC6899610 DOI: 10.1002/humu.23863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/19/2022]
Abstract
Hemoglobinopathies are the most common monogenic disorders worldwide. Substantial effort has been made to establish databases to record complete mutation spectra causing or modifying this group of diseases. We present a variant database which couples an online auxiliary diagnosis and at-risk assessment system for hemoglobinopathies (DASH). The database was integrated into the Leiden Open Variation Database (LOVD), in which we included all reported variants focusing on a Chinese population by literature peer review-curation and existing databases, such as HbVar and IthaGenes. In addition, comprehensive mutation data generated by high-throughput sequencing of 2,087 hemoglobinopathy patients and 20,222 general individuals from southern China were also incorporated into the database. These sequencing data enabled us to observe disease-causing and modifier variants responsible for hemoglobinopathies in bulk. Currently, 371 unique variants have been recorded; 265 of 371 were described as disease-causing variants, whereas 106 were defined as modifier variants, including 34 functional variants identified by a quantitative trait association study of this high-throughput sequencing data. Due to the availability of a comprehensive phenotype-genotype data set, DASH has been established to automatically provide accurate suggestions on diagnosis and genetic counseling of hemoglobinopathies. LOVD-DASH will inspire us to deal with clinical genotyping and molecular screening for other Mendelian disorders.
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Affiliation(s)
- Li Zhang
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Qianqian Zhang
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | | | - Peikuan Cong
- Institute for Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuhua Ye
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Shiping Chen
- BGI Clinical Laboratories-Shenzhen, Shenzhen, Guangdong, China
| | - Xinhua Zhang
- Department of Hematopathology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yan Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Baosheng Zhu
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Wangwei Cai
- School of Basic Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Shaoke Chen
- Department of Pediatrics, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xiaoling Guo
- Department of Pediatrics, Maternity and Child Health Care Hospital of Foshan City, Foshan, Guangdong, China
| | - Chonglin Zhang
- Department of Clinical Laboratory, Guilin Women and Children health care hospital, Guilin, Guangxi, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternity and Child Healthcare Hospital, Zhuhai, Guangdong, China
| | - Jie Zou
- Department of Clinical Laboratory, Maternal and Child Health Hospital in Meizhou, Meizhou, Guangdong, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Biyan Chen
- Department of Clinical Laboratory, Baise Women and Children Care Hospital, Baise, Guangxi, China
| | - Shanhuo Yan
- Department of Clinical Laboratory, Qinzhou Maternal and Child Health Hospital, Qinzhou, Guangxi, China
| | - Yajun Chen
- Center For Prenatal Diagnosis Shaoguan, Shaoguan Municipal Maternity and Child Healthcare Hospital, Guangdong, China
| | - Yuehong Zhou
- Department of Clinical Laboratory, The People's Hospital of Yunfu City, Yunfu, Guangdong, China
| | - Hongmei Ding
- Department of Clinical Laboratory, Pingguo Women and Children Care Hospital, Baise, Guangxi, China
| | - Xiarong Li
- Beijing GeneDock Technology Company, Beijing, China
| | - Dianyu Chen
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmei Zhong
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Xuan Shang
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Xuanzhu Liu
- Beijing GeneDock Technology Company, Beijing, China
| | - Ming Qi
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Center for Genetic & Genomic Medicine, JamesWatson Institute of Genome Sciences, Zhejiang University Medical School 1st Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Xiangmin Xu
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
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27
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Ekong R, Vihinen M. Checklist for gene/disease-specific variation database curators to enable ethical data management. Hum Mutat 2019; 40:1634-1640. [PMID: 31347738 DOI: 10.1002/humu.23881] [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: 04/17/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 11/10/2022]
Abstract
Databases with variant and phenotype information are essential for advancing research and improving the health and welfare of individuals. These resources require data to be collected, curated, and shared among relevant specialties to maximize impact. The increasing generation of data which must be shared both nationally and globally for maximal effect presents important ethical and privacy concerns. Database curators need to ensure that their work conform to acceptable ethical standards. A Working Group of the Human Variome Project had the task of updating and streamlining ethical guidelines for locus-specific/gene variant database curators. In this article, we present practical and achievable steps which should assist database curators in carrying out their responsibilities within acceptable ethical norms.
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Affiliation(s)
- Rosemary Ekong
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, Lund, Sweden
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28
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Katsila T, Balasopoulou A, Tsagaraki I, Patrinos GP. Pharmacomicrobiomics informs clinical pharmacogenomics. Pharmacogenomics 2019; 20:731-739. [PMID: 31368841 DOI: 10.2217/pgs-2019-0027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.
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Affiliation(s)
- Theodora Katsila
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece.,Institute of Chemical Biology, National Hellenic Research Centre, Athens, Greece
| | - Angeliki Balasopoulou
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - Ioanna Tsagaraki
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece.,Department of Pathology, College of Medicine & Health Sciences, Al Ain, United Arab Emirates.,Zayed Center of Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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29
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30
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Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing. Blood 2018; 131:2915-2928. [PMID: 29789357 DOI: 10.1182/blood-2018-03-838540] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Disorders involving β-globin gene mutations, primarily β-thalassemia and sickle cell disease, represent a major target for hematopoietic stem/progenitor cell (HSPC) gene therapy. This includes CRISPR/Cas9-mediated genome editing approaches in adult CD34+ cells aimed toward the reactivation of fetal γ-globin expression in red blood cells. Because models involving erythroid differentiation of CD34+ cells have limitations in assessing γ-globin reactivation, we focused on human β-globin locus-transgenic (β-YAC) mice. We used a helper-dependent human CD46-targeting adenovirus vector expressing CRISPR/Cas9 (HDAd-HBG-CRISPR) to disrupt a repressor binding region within the γ-globin promoter. We transduced HSPCs from β-YAC/human CD46-transgenic mice ex vivo and subsequently transplanted them into irradiated recipients. Furthermore, we used an in vivo HSPC transduction approach that involves HSPC mobilization and the intravenous injection of HDAd-HBG-CRISPR into β-YAC/CD46-transgenic mice. In both models, we demonstrated efficient target site disruption, resulting in a pronounced switch from human β- to γ-globin expression in red blood cells of adult mice that was maintained after secondary transplantation of HSPCs. In long-term follow-up studies, we did not detect hematological abnormalities, indicating that HBG promoter editing does not negatively affect hematopoiesis. This is the first study that shows successful in vivo HSPC genome editing by CRISPR/Cas9.
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31
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Philipsen S, Hardison RC. Evolution of hemoglobin loci and their regulatory elements. Blood Cells Mol Dis 2018; 70:2-12. [PMID: 28811072 PMCID: PMC5807248 DOI: 10.1016/j.bcmd.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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32
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Holub P, Kohlmayer F, Prasser F, Mayrhofer MT, Schlünder I, Martin GM, Casati S, Koumakis L, Wutte A, Kozera Ł, Strapagiel D, Anton G, Zanetti G, Sezerman OU, Mendy M, Valík D, Lavitrano M, Dagher G, Zatloukal K, van Ommen GB, Litton JE. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. Biopreserv Biobank 2018; 16:97-105. [PMID: 29359962 PMCID: PMC5906729 DOI: 10.1089/bio.2017.0110] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability-entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)-are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.
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Affiliation(s)
| | | | | | | | | | | | - Sara Casati
- BBMRI.it and Universita degli Studi di Milano-Bicocca, Milano, Italy
| | - Lefteris Koumakis
- BBMRI.gr and Foundation for Research and Technology-Hellas, Heraklion, Greece
| | | | - Łukasz Kozera
- BBMRI.pl and Wroclaw Research Centre EIT+, Wroclaw, Poland
| | | | | | | | | | - Maimuna Mendy
- BBMRI.IARC and International Agency for Research on Cancer, Lyon, France
| | - Dalibor Valík
- BBMRI.cz and Masaryk Memorial Cancer Institute, Brno, Czech Republic
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33
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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34
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Chondrou V, Kolovos P, Sgourou A, Kourakli A, Pavlidaki A, Kastrinou V, John A, Symeonidis A, Ali BR, Papachatzopoulou A, Katsila T, Patrinos GP. Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β-type hemoglobinopathy patients. Hum Genomics 2017; 11:24. [PMID: 29061162 PMCID: PMC5654038 DOI: 10.1186/s40246-017-0120-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/16/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Human erythropoiesis is characterized by distinct gene expression profiles at various developmental stages. Previous studies suggest that fetal-to-adult hemoglobin switch is regulated by a complex mechanism, in which many key players still remain unknown. Here, we report our findings from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue. RESULTS From our in-depth data analysis, pathway analysis, and text mining, we opted to focus on the VEGFA gene, given its gene expression characteristics. Selected VEGFA genomic variants, identified through linkage disequilibrium analysis, were explored further for their association with elevated fetal hemoglobin levels in β-type hemoglobinopathy patients. Our downstream analysis of non-transfusion-dependent β-thalassemia patients, β-thalassemia major patients, compound heterozygous sickle cell disease/β-thalassemia patients receiving hydroxyurea as fetal hemoglobin augmentation treatment, and non-thalassemic individuals indicated that VEGFA genomic variants were associated with disease severity in β-thalassemia patients and hydroxyurea treatment efficacy in SCD/β-thalassemia compound heterozygous patients. CONCLUSIONS Our findings suggest that VEGFA may act as a modifier gene of human globin gene expression and, at the same time, serve as a genomic biomarker in β-type hemoglobinopathy disease severity and hydroxyurea treatment efficacy.
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Affiliation(s)
- Vasiliki Chondrou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece
| | - Petros Kolovos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Alexandra Kourakli
- Hematology Division, Department of Internal Medicine, Faculty of Medicine, University of Patras, Patras, Greece
| | - Alexia Pavlidaki
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece.,Present address: Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMC/CNRS/INSERM/UDS, 67404 ILLKIRCH, BP 10142, CU de Strasbourg, France
| | - Vlasia Kastrinou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece
| | - Anne John
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Argiris Symeonidis
- Hematology Division, Department of Internal Medicine, Faculty of Medicine, University of Patras, Patras, Greece
| | - Bassam R Ali
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece. .,Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. .,Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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Farashi S, Harteveld CL. Molecular basis of α-thalassemia. Blood Cells Mol Dis 2017; 70:43-53. [PMID: 29032940 DOI: 10.1016/j.bcmd.2017.09.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 02/05/2023]
Abstract
α-Thalassemia is an inherited, autosomal recessive, disorder characterized by a microcytic hypochromic anemia. It is one of the most common monogenic gene disorders in the world population. The clinical severity varies from almost asymptomatic, to mild microcytic hypochromic, and to a lethal hemolytic condition, called Hb Bart's Hydrops Foetalis Syndrome. The molecular basis are usually deletions and less frequently, point mutations affecting the expression of one or more of the duplicated α-genes. The clinical variation and increase in disease severity is directly related to the decreased expression of one, two, three or four copies of the α-globin genes. Deletions and point mutations in the α-globin genes and their regulatory elements have been studied extensively in carriers and patients and these studies have given insight into the α-globin genes are regulated. By looking at naturally occurring deletions and point mutations, our knowledge of globin-gene regulation and expression will continue to increase and will lead to new targets of therapy.
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Affiliation(s)
- Samaneh Farashi
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelis L Harteveld
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands.
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36
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Increasing the involvement of diverse populations in genomics-based health care-lessons from haemoglobinopathies. J Community Genet 2017; 8:311-318. [PMID: 28879424 DOI: 10.1007/s12687-017-0327-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/23/2017] [Indexed: 01/21/2023] Open
Abstract
Integrating genomic medicine into health care delivery poses significant challenges to health professionals. To draw clinical benefit from genomic information, there is a need to build an evidence-based relationship between genotype and the physical expression of that genomic information. The work presented here uses preliminary work in the field of haemoglobinopathies to address two important challenges: to ensure that health care professionals in low- and middle-income countries are actively involved in the processes that will support genomic medicine, and that equity and diversity concerns are met so that clinical services can have relevance across all population and sub-population groups. Haemoglobinopathies provide an opportunity for gaining a better understanding of how long-standing genetic knowledge can be leveraged to determine if genomic-based services can be beneficial in low-resource settings. The Global Globin 2020 Challenge (GG2020) is an international initiative that uses haemoglobinopathies as an entry point to achieving growth in the quality and quantity of curated inputs into internationally recognised databases, harmonising the sharing of variant information within and between countries for better health care delivery and ensuring that storing, curation and sharing of variant information become an integral part of health care. Early findings from GG2020 indicate that paying attention to population diversity is an integral part of prevention and control of haemoglobinopathies.
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Shang X, Peng Z, Ye Y, Asan, Zhang X, Chen Y, Zhu B, Cai W, Chen S, Cai R, Guo X, Zhang C, Zhou Y, Huang S, Liu Y, Chen B, Yan S, Chen Y, Ding H, Yin X, Wu L, He J, Huang D, He S, Yan T, Fan X, Zhou Y, Wei X, Zhao S, Cai D, Guo F, Zhang Q, Li Y, Zhang X, Lu H, Huang H, Guo J, Zhu F, Yuan Y, Zhang L, Liu N, Li Z, Jiang H, Zhang Q, Zhang Y, Juhari WKW, Hanafi S, Zhou W, Xiong F, Yang H, Wang J, Zilfalil BA, Qi M, Yang Y, Yin Y, Mao M, Xu X. Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies. EBioMedicine 2017; 23:150-159. [PMID: 28865746 PMCID: PMC5605365 DOI: 10.1016/j.ebiom.2017.08.015] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 12/17/2022] Open
Abstract
Hemoglobinopathies are among the most common autosomal-recessive disorders worldwide. A comprehensive next-generation sequencing (NGS) test would greatly facilitate screening and diagnosis of these disorders. An NGS panel targeting the coding regions of hemoglobin genes and four modifier genes was designed. We validated the assay by using 2522 subjects affected with hemoglobinopathies and applied it to carrier testing in a cohort of 10,111 couples who were also screened through traditional methods. In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis. In the molecular screening analysis of the 10,111 couples, we detected 4180 individuals in total who carried 4840 mutant alleles, and identified 186 couples at risk of having affected offspring. 12.1% of the pathogenic or likely pathogenic variants identified by our NGS assay, which were undetectable by traditional methods. Compared with the traditional methods, our assay identified an additional at-risk 35 couples. We describe a comprehensive NGS-based test that offers advantages over the traditional screening/molecular testing methods. To our knowledge, this is among the first large-scale population study to systematically evaluate the application of an NGS technique in carrier screening and molecular diagnosis of hemoglobinopathies.
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Affiliation(s)
- Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Yuhua Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Asan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xinhua Zhang
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Baosheng Zhu
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shaoke Chen
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xiaoling Guo
- Maternity and Child Health Care Hospital of Foshan City, Foshan, Guangdong, China
| | - Chonglin Zhang
- Guilin Women and Children health care hospital, Guilin, Guangxi, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai Institute of Medical Genetics, Zhuhai, Guangdong, China
| | - Shuodan Huang
- Maternal and Child Health Hospital in Meizhou, Meizhou, Guangdong, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dong Guan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Biyan Chen
- Baise Women and Children Care Hospital, Baise, Guangxi, China
| | - Shanhuo Yan
- Genetic Laboratory, Qinzhou Maternaland Child Health Hospital, Qingzhou, Guangxi, China
| | - Yajun Chen
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, China
| | - Hongmei Ding
- Department of Gynecology and Obstetrics, The People's Hospital of Yunfu City, Yunfu, Guangdong, China
| | - Xiaolin Yin
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Liusong Wu
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Jing He
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Dongai Huang
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Sheng He
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xin Fan
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Yuehong Zhou
- Pingguo Women and Children Care Hospital, Baise, Guangxi, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Sumin Zhao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Decheng Cai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yun Li
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xuelian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Haorong Lu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huajie Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Junfu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Fei Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Li Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Na Liu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhiming Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Hui Jiang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Qiang Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yijia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | | | - Sarifah Hanafi
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Bin Alwi Zilfalil
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Ming Qi
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Center for Genetic & Genomic Medicine, Zhejiang University Medical School 1st Affiliated Hospital, James Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Yaping Yang
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Ye Yin
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Mao Mao
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China.
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Messner DA, Koay P, Al Naber J, Cook-Deegan R, Majumder M, Javitt G, Dvoskin R, Bollinger J, Curnutte M, McGuire AL. Barriers to clinical adoption of next-generation sequencing: a policy Delphi panel's solutions. Per Med 2017; 14:339-354. [PMID: 29230253 DOI: 10.2217/pme-2016-0104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Aim Identify solutions to the most important policy barriers to the clinical adoption of next-generation sequencing. Materials & methods Four-round modified policy Delphi with a multistakeholder panel of 48 experts. The panel deliberated policy solutions to (previously reported) challenges deemed most important to address. Results The group advocated using consensus panels to promote consistency in payer policies and to standardize test reporting, and favored making genomic data-sharing a condition of regulatory clearance, certification, or accreditation processes. They were split on the role of US FDA. Conclusion Panelists found common ground on solutions for health plan coverage policy consistency, data-sharing, and standardizing reporting, but were sharply divided on the role of the FDA in mitigating risks to patients.
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Affiliation(s)
- Donna A Messner
- Center for Medical Technology Policy, Baltimore, MD 21202, USA
| | - Pei Koay
- Center for Medical Technology Policy, Baltimore, MD 21202, USA
| | | | - Robert Cook-Deegan
- School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, AZ 85281, USA
| | - Mary Majumder
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gail Javitt
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Dvoskin
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Juli Bollinger
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret Curnutte
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy L McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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Molecular basis of β thalassemia and potential therapeutic targets. Blood Cells Mol Dis 2017; 70:54-65. [PMID: 28651846 DOI: 10.1016/j.bcmd.2017.06.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/15/2022]
Abstract
The remarkable phenotypic diversity of β thalassemia that range from severe anemia and transfusion-dependency, to a clinically asymptomatic state exemplifies how a spectrum of disease severity can be generated in single gene disorders. While the genetic basis for β thalassemia, and how severity of the anemia could be modified at different levels of its pathophysiology have been well documented, therapy remains largely supportive with bone marrow transplant being the only cure. Identification of the genetic variants modifying fetal hemoglobin (HbF) production in combination with α globin genotype provide some prediction of disease severity for β thalassemia but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered. Nonetheless, genetic studies have been successful in characterizing the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation. BCL11A has been established as a quantitative repressor, and progress has been made in manipulating its expression using genomic and gene-editing approaches for therapeutic benefits. Recent discoveries and understanding in the mechanisms associated with ineffective and abnormal erythropoiesis have also provided additional therapeutic targets, a couple of which are currently being tested in clinical trials.
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Vis DJ, Lewin J, Liao RG, Mao M, Andre F, Ward RL, Calvo F, Teh BT, Camargo AA, Knoppers BM, Sawyers CL, Wessels LFA, Lawler M, Siu LL, Voest E. Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape. Ann Oncol 2017; 28:1145-1151. [PMID: 28453708 PMCID: PMC5406763 DOI: 10.1093/annonc/mdx037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. METHODS A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally. Additionally, respondents were asked as to provide the primary intent of their initiative (clinical diagnostic, research or combination). RESULTS Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (P = 0.03) and whole genome sequencing (P = 0.01) were utilized less frequently in clinical diagnostic than in research initiatives. Procedures to identify cancer-specific variants were heterogeneous, with bioinformatics pipelines employing different mutation calling/variant annotation algorithms. Measurement of treatment efficacy varied amongst initiatives, with time on treatment (57%) and RECIST (53%) being the most common; however, other parameters were also employed. Whilst 72% of initiatives indicated data sharing, its scope varied, with a number of restrictions in place (e.g. transfer of raw data). The largest perceived barriers to data harmonization were the lack of financial support (P < 0.01) and bioinformatics concerns (e.g. lack of interoperability) (P = 0.02). Capturing clinical data was more likely to be perceived as a barrier to data sharing by larger initiatives than by smaller initiatives (P = 0.01). CONCLUSIONS These results identify the main barriers, as perceived by the cancer sequencing community, to effective sharing of cancer genomic and clinical data. They highlight the need for greater harmonization of technical, ethical and data capture processes in cancer sample sequencing worldwide, in order to support effective and responsible data sharing for the benefit of patients.
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Affiliation(s)
- D. J. Vis
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J. Lewin
- Princess Margaret Cancer Centre, Toronto, Canada
| | - R. G. Liao
- Global Alliance for Genomics and Health, Broad Institute, Cambridge, USA
| | - M. Mao
- Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - F. Andre
- INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif, France
| | - R. L. Ward
- Research, University of Queensland, Brisbane, Australia
| | - F. Calvo
- Cancer Core Europe, Gustave Roussy, Villejuif, France
| | | | | | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - C. L. Sawyers
- Memorial Sloan Kettering Cancer Centre, New York, USA
| | - L. F. A. Wessels
- Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Bioinformatics & Statistics, Delft University of Technology, Delft, The Netherlands
| | - M. Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - L. L. Siu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - E. Voest
- Netherlands Cancer Institute, Amsterdam, The Netherlands
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Lee WS, McColl B, Maksimovic J, Vadolas J. Epigenetic interplay at the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:393-404. [DOI: 10.1016/j.bbagrm.2017.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 02/02/2023]
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Mañú Pereira MDM, Ropero P, Loureiro C, Vives Corrons JL. Low affinity hemoglobinopathy (Hb Vigo) due to a new mutation of beta globin gene (c200 A>T; Lys>Ile). A cause of rare anemia misdiagnosis. Am J Hematol 2017; 92:E38-E40. [PMID: 28066926 DOI: 10.1002/ajh.24649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 11/07/2022]
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Faggioni M, Baber U, Sartori S, Giustino G, Cohen DJ, Henry TD, Farhan S, Ariti C, Dangas G, Gibson M, Giacoppo D, Krucoff MW, Aquino M, Chandrasekhar J, Moliterno DJ, Colombo A, Vogel B, Chieffo A, Kini AS, Witzenbichler B, Weisz G, Steg PG, Pocock S, Mehran R. Incidence, Patterns, and Associations Between Dual-Antiplatelet Therapy Cessation and Risk for Adverse Events Among Patients With and Without Diabetes Mellitus Receiving Drug-Eluting Stents. JACC Cardiovasc Interv 2017; 10:645-654. [DOI: 10.1016/j.jcin.2016.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 12/13/2022]
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Zaldívar-López S, Rowell JL, Fiala EM, Zapata I, Couto CG, Alvarez CE. Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. BMC Genomics 2017; 18:141. [PMID: 28178945 PMCID: PMC5299747 DOI: 10.1186/s12864-017-3513-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The main function of hemoglobin (Hb) is to transport oxygen in the circulation. It is among the most highly studied proteins due to its roles in physiology and disease, and most of our understanding derives from comparative research. There is great diversity in Hb gene evolution in placental mammals, mostly in the repertoire and regulation of the β-globin subunits. Dogs are an ideal model in which to study Hb genes because: 1) they are members of Laurasiatheria, our closest relatives outside of Euarchontoglires (including primates, rodents and rabbits), 2) dog breeds are isolated populations with their own Hb-associated genetics and diseases, and 3) their high level of health care allows for development of biomedical investigation and translation. Results We established that dogs have a complement of five α and five β-globin genes, all of which can be detected as spliced mRNA in adults. Strikingly, HBD, the allegedly-unnecessary adult β-globin protein in humans, is the primary adult β-globin in dogs and other carnivores; moreover, dogs have two active copies of the HBD gene. In contrast, the dominant adult β-globin of humans, HBB, has high sequence divergence and is expressed at markedly lower levels in dogs. We also showed that canine HBD and HBB genes are complex chimeras that resulted from multiple gene conversion events between them. Lastly, we showed that the strongest signal of evolutionary selection in a high-altitude breed, the Bernese Mountain Dog, lies in a haplotype block that spans the β-globin locus. Conclusions We report the first molecular genetic characterization of Hb genes in dogs. We found important distinctions between adult β-globin expression in carnivores compared to other members of Laurasiatheria. Our findings are also likely to raise new questions about the significance of human HBD. The comparative genomics of dog hemoglobin genes sets the stage for diverse research and translation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3513-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Zaldívar-López
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: SZL, Departamento. de Genetica, Facultad de Veterinaria, Universidad de Cordoba, Cordoba, Spain
| | - Jennie L Rowell
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Nursing, The Ohio State University, Columbus, OH, USA.,Present affiliation: Center of Excellence in Critical and Complex Care, College of Nursing, The Ohio State University, Columbus, USA
| | - Elise M Fiala
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Isain Zapata
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - C Guillermo Couto
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: Couto Veterinary Consultants, Hilliard, OH, USA
| | - Carlos E Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA. .,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA. .,College of Medicine, The Ohio State University, Columbus, OH, USA.
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45
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Traeger-Synodinos J, Harteveld CL. Preconception carrier screening and prenatal diagnosis in thalassemia and hemoglobinopathies: challenges and future perspectives. Expert Rev Mol Diagn 2017; 17:281-291. [DOI: 10.1080/14737159.2017.1285701] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Joanne Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, Athens, Greece
| | - Cornelis L. Harteveld
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden, The Netherlands
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46
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Thein SL. Genetic Basis and Genetic Modifiers of β-Thalassemia and Sickle Cell Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1013:27-57. [PMID: 29127676 DOI: 10.1007/978-1-4939-7299-9_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-thalassemia and sickle cell disease (SCD) are prototypical Mendelian single gene disorders, both caused by mutations affecting the adult β-globin gene. Despite the apparent genetic simplicity, both disorders display a remarkable spectrum of phenotypic severity and share two major genetic modifiers-α-globin genotype and innate ability to produce fetal hemoglobin (HbF, α2γ2).This article provides an overview of the genetic basis for SCD and β-thalassemia, and genetic modifiers identified through phenotype correlation studies. Identification of the genetic variants modifying HbF production in combination with α-globin genotype provide some prediction of disease severity for β-thalassemia and SCD but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered.Nonetheless, genetic studies have been successful in characterizing some of the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation.
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Affiliation(s)
- Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Building 10, Room 6S241 MSC 1589, 10 Center Dr., Bethesda, MD, 20892-1589, USA.
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47
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Ludwig LS, Khajuria RK, Sankaran VG. Emerging cellular and gene therapies for congenital anemias. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:332-348. [PMID: 27792859 DOI: 10.1002/ajmg.c.31529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Congenital anemias comprise a group of blood disorders characterized by a reduction in the number of peripherally circulating erythrocytes. Various genetic etiologies have been identified that affect diverse aspects of erythroid physiology and broadly fall into two main categories: impaired production or increased destruction of mature erythrocytes. Current therapies are largely focused on symptomatic treatment and are often based on transfusion of donor-derived erythrocytes and management of complications. Hematopoietic stem cell transplantation represents the only curative option currently available for the majority of congenital anemias. Recent advances in gene therapy and genome editing hold promise for the development of additional curative strategies for these blood disorders. The relative ease of access to the hematopoietic stem cell compartment, as well as the possibility of genetic manipulation ex vivo and subsequent transplantation in an autologous manner, make blood disorders among the most amenable to cellular therapies. Here we review cell-based and gene therapy approaches, and discuss the limitations and prospects of emerging avenues, including genome editing tools and the use of pluripotent stem cells, for the treatment of congenital forms of anemia. © 2016 Wiley Periodicals, Inc.
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48
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Viennas E, Komianou A, Mizzi C, Stojiljkovic M, Mitropoulou C, Muilu J, Vihinen M, Grypioti P, Papadaki S, Pavlidis C, Zukic B, Katsila T, van der Spek PJ, Pavlovic S, Tzimas G, Patrinos GP. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2016; 45:D846-D853. [PMID: 27924022 PMCID: PMC5210643 DOI: 10.1093/nar/gkw949] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023] Open
Abstract
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications.
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Affiliation(s)
- Emmanouil Viennas
- University of Patras, Faculty of Engineering, Department of Computer Engineering and Informatics, GR-26504, Patras, Greece
| | - Angeliki Komianou
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Clint Mizzi
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands.,University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Laboratory of Molecular Biomedicine, 11010, Belgrade, Serbia
| | | | - Juha Muilu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-22100, Lund, Sweden
| | - Panagiota Grypioti
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Styliani Papadaki
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Cristiana Pavlidis
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Branka Zukic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Peter J van der Spek
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
| | - Sonja Pavlovic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Giannis Tzimas
- Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-30020, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece .,Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
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49
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Mizzi C, Dalabira E, Kumuthini J, Dzimiri N, Balogh I, Başak N, Böhm R, Borg J, Borgiani P, Bozina N, Bruckmueller H, Burzynska B, Carracedo A, Cascorbi I, Deltas C, Dolzan V, Fenech A, Grech G, Kasiulevicius V, Kádaši Ľ, Kučinskas V, Khusnutdinova E, Loukas YL, Macek M, Makukh H, Mathijssen R, Mitropoulos K, Mitropoulou C, Novelli G, Papantoni I, Pavlovic S, Saglio G, Setric J, Stojiljkovic M, Stubbs AP, Squassina A, Torres M, Turnovec M, van Schaik RH, Voskarides K, Wakil SM, Werk A, del Zompo M, Zukic B, Katsila T, Lee MTM, Motsinger-Rief A, Mc Leod HL, van der Spek PJ, Patrinos GP. A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics. PLoS One 2016; 11:e0162866. [PMID: 27636550 PMCID: PMC5026342 DOI: 10.1371/journal.pone.0162866] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/30/2016] [Indexed: 12/26/2022] Open
Abstract
Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes. Our data show significant inter-population pharmacogenomic biomarker allele frequency differences, particularly in 7 clinically actionable pharmacogenomic biomarkers in 7 European populations, affecting drug efficacy and/or toxicity of 51 medication treatment modalities. These data also reflect on the differences observed in the prevalence of high-risk genotypes in these populations, as far as common markers in the CYP2C9, CYP2C19, CYP3A5, VKORC1, SLCO1B1 and TPMT pharmacogenes are concerned. Also, our data demonstrate notable differences in predicted genotype-based warfarin dosing among these populations. Our findings can be exploited not only to develop guidelines for medical prioritization, but most importantly to facilitate integration of pharmacogenomics and to support pre-emptive pharmacogenomic testing. This may subsequently contribute towards significant cost-savings in the overall healthcare expenditure in the participating countries, where pharmacogenomics implementation proves to be cost-effective.
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Affiliation(s)
- Clint Mizzi
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, Msida, Malta
| | - Eleni Dalabira
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Judit Kumuthini
- Center for Proteomic and Genomic Research, Observatory, Cape Town, South Africa
| | - Nduna Dzimiri
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | | | - Ruwen Böhm
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Joseph Borg
- University of Malta, Department of Applied Biomedical Science, Faculty of Health Sciences, Msida, Malta
| | - Paola Borgiani
- University of Rome “Tor Vergata”, Department of Biomedicine and Prevention, Rome, Italy
| | | | - Henrike Bruckmueller
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Beata Burzynska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Ingolf Cascorbi
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Constantinos Deltas
- University of Cyprus, Molecular Medicine Research Center, Department of Biological Sciences, Nicosia, Cyprus
| | - Vita Dolzan
- University of Ljubljana Faculty of Medicine, Ljubljana, Slovenia
| | - Anthony Fenech
- University of Malta, Faculty of Medicine, Department of Surgery, Msida, Malta
| | - Godfrey Grech
- University of Malta, Faculty of Medicine, Department of Surgery, Msida, Malta
| | - Vytautas Kasiulevicius
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ľudevít Kádaši
- Comenius University, Faculty of Natural Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Yiannis L. Loukas
- University of Athens, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Athens, Greece
| | - Milan Macek
- Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Halyna Makukh
- Institute of Hereditary Pathology, Ukrainian National Academy of Medical Sciences, Lviv, Ukraine
| | - Ron Mathijssen
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | | | - Christina Mitropoulou
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | - Giuseppe Novelli
- University of Rome “Tor Vergata”, Department of Biomedicine and Prevention, Rome, Italy
| | - Ioanna Papantoni
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | | | - Jadranka Setric
- University Hospital Centre, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | - Andrew P. Stubbs
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
| | - Alessio Squassina
- University of Cagliari, Department of Biomedical Sciences, Cagliari, Italy
| | - Maria Torres
- University of Santiago de Compostela, Santiago, Spain
| | - Marek Turnovec
- Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Ron H. van Schaik
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | - Konstantinos Voskarides
- University of Cyprus, Molecular Medicine Research Center, Department of Biological Sciences, Nicosia, Cyprus
| | - Salma M. Wakil
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anneke Werk
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Maria del Zompo
- University of Cagliari, Department of Biomedical Sciences, Cagliari, Italy
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | - Theodora Katsila
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Ming Ta Michael Lee
- RIKEN Institute, Center for Genomic Medicine, Laboratory for International Alliance, Yokohama, Japan
| | - Alison Motsinger-Rief
- North Carolina State University, Department of Statistics, Raleigh, NC, United States of America
| | | | - Peter J. van der Spek
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
| | - George P. Patrinos
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
- * E-mail:
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50
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Harteveld CL, Pissard S, Korver AMH, Riou J, Legac E, Lansbergen G, Pardijs IL, Giordano PC, Versteegh FGA. Hb Olivet (HBA1: C.40G > A; p.Ala14Thr), a Novel Silent Hemoglobin Variant in Two Families of Distinct Origin. Hemoglobin 2016; 40:349-352. [PMID: 27624280 DOI: 10.1080/03630269.2016.1210160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We report two families, members of which are carriers of a novel hemoglobin (Hb) variant that was named Hb Olivet [α13(A11)Ala→Thr (α1) (GCC > ACC); HBA1: c.40G > A; p.Ala14Thr]. The analysis of these cases allowed a clear description of this anomaly that behaves as a silent Hb. In the first family, of Portuguese ethnicity living in France, the proband, a 24-year-old male and his 57-year-old mother, both appeared to be carriers. The son presented with borderline mean corpuscular volume (MCV), while the mother was normocytic and normochromic. Hemoglobin separation on capillary electrophoresis (CE) was normal, while a slightly asymmetric peak was observed on high performance liquid chromatography (HPLC). In a second family, originally from Surinam but living in The Netherlands, the proband, a 6-year-old girl, showed a mild microcytosis at low ferritin levels. The abnormal Hb was inherited from the mother who was clearly iron depleted, was not present in the sister and brother of the proband. The microcytic hypochromic anemia was only shown in two out of a total of four carriers. It therefore seems likely that iron depletion is causative as two carriers are completely normal. Characterization and genotype/phenotype correlation are briefly described.
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Affiliation(s)
- Cornelis L Harteveld
- a Hemoglobinopathies Laboratory, Department of Human and Clinical Genetics , Leiden University Medical Center (LUMC) , Leiden , the Netherlands
| | - Serge Pissard
- b Laboratory of Genetics , Assistance Publique-Hôitaux De Paris (APHP), Groupe Hospitalier Universitaire (GHU) Henri Mondor, Universite Paris Est Créteil (UPEC) and Inserm Institut Mondor De Recherche Biologique (IMRB) U955eq2 , Créteil , France
| | - Anna M H Korver
- c Department of Pediatrics , Groene Hart Hospital , Gouda , the Netherlands
| | - Jean Riou
- d Laboratory of Genetics , Assistance Publique-Hôitaux De Paris (APHP), Groupe Hospitalier Universitaire (GHU) Henri Mondor , Créteil , France
| | - Eric Legac
- e Laboratory of Biology , Centre Hospitalier Régioonale (CHR) Orleans , Orleans , France
| | - Gideon Lansbergen
- f Clinical Chemistry, Groene Hart Hospital , Gouda , the Netherlands
| | - Inge L Pardijs
- c Department of Pediatrics , Groene Hart Hospital , Gouda , the Netherlands.,g General Practitioner , Gouda , the Netherlands
| | - Piero C Giordano
- a Hemoglobinopathies Laboratory, Department of Human and Clinical Genetics , Leiden University Medical Center (LUMC) , Leiden , the Netherlands
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