1
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Schuermans N, El Chehadeh S, Hemelsoet D, Gautheron J, Vantyghem MC, Nouioua S, Tazir M, Vigouroux C, Auclair M, Bogaert E, Dufour S, Okawa F, Hilbert P, Van Doninck N, Taquet MC, Rosseel T, De Clercq G, Debackere E, Van Haverbeke C, Cherif FR, Urtizberea JA, Chanson JB, Funalot B, Authier FJ, Kaya S, Terryn W, Callens S, Depypere B, Van Dorpe J, Poppe B, Impens F, Mizushima N, Depienne C, Jéru I, Dermaut B. Loss of phospholipase PLAAT3 causes a mixed lipodystrophic and neurological syndrome due to impaired PPARγ signaling. Nat Genet 2023; 55:1929-1940. [PMID: 37919452 DOI: 10.1038/s41588-023-01535-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/16/2023] [Indexed: 11/04/2023]
Abstract
Phospholipase A/acyltransferase 3 (PLAAT3) is a phospholipid-modifying enzyme predominantly expressed in neural and white adipose tissue (WAT). It is a potential drug target for metabolic syndrome, as Plaat3 deficiency in mice protects against diet-induced obesity. We identified seven patients from four unrelated consanguineous families, with homozygous loss-of-function variants in PLAAT3, who presented with a lipodystrophy syndrome with loss of fat varying from partial to generalized and associated with metabolic complications, as well as variable neurological features including demyelinating neuropathy and intellectual disability. Multi-omics analysis of mouse Plaat3-/- and patient-derived WAT showed enrichment of arachidonic acid-containing membrane phospholipids and a strong decrease in the signaling of peroxisome proliferator-activated receptor gamma (PPARγ), the master regulator of adipocyte differentiation. Accordingly, CRISPR-Cas9-mediated PLAAT3 inactivation in human adipose stem cells induced insulin resistance, altered adipocyte differentiation with decreased lipid droplet formation and reduced the expression of adipogenic and mature adipocyte markers, including PPARγ. These findings establish PLAAT3 deficiency as a hereditary lipodystrophy syndrome with neurological manifestations, caused by a PPARγ-dependent defect in WAT differentiation and function.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale, UMRS_1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | | | - Jérémie Gautheron
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Marie-Christine Vantyghem
- Endocrinology, Diabetology, Metabolism Department, National Competence Centre for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Lille University Hospital, Lille, France
- University of Lille, INSERM U1190, European Genomic Institute for Diabetes, Lille, France
| | - Sonia Nouioua
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | - Meriem Tazir
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
- Department of Neurology, CHU Algiers (Mustapha Pacha Hospital), Algiers, Algeria
| | - Corinne Vigouroux
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Martine Auclair
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sara Dufour
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Fumiya Okawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Pascale Hilbert
- Department of Molecular and Cellular Biology, Institute of Pathology and Genetics, Charleroi, Belgium
| | - Nike Van Doninck
- Department of Endocrinology and Diabetology, General Hospital VITAZ, Sint-Niklaas, Belgium
| | - Marie-Caroline Taquet
- Department of Internal Medicine and Nutrition, Hopitaux Universitaires Strasbourg, Strasbourg, France
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Griet De Clercq
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | | - Ferroudja Ramdane Cherif
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | | | - Jean-Baptiste Chanson
- Service de Neurologie et Centre de Référence Neuromusculaire Nord/Est/Ile de France, Hôpital de Hautepierre, Strasbourg, France
| | - Benoit Funalot
- Department of Medical Genetics, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
| | - François-Jérôme Authier
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
- Centre Expert de Pathologie Neuromusculaire/Histologie, Département de Pathologie, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
| | - Sabine Kaya
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Wim Terryn
- Department of Nephrology, Jan Yperman Hospital, Ieper, Belgium
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bernard Depypere
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Christel Depienne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Isabelle Jéru
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Department of Medical Genetics, DMU BioGeM, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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2
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Guillemyn B, De Saffel H, Bek JW, Tapaneeyaphan P, De Clercq A, Jarayseh T, Debaenst S, Willaert A, De Rycke R, Byers PH, Rosseel T, Coucke P, Blaumeiser B, Syx D, Malfait F, Symoens S. Syntaxin 18 Defects in Human and Zebrafish Unravel Key Roles in Early Cartilage and Bone Development. J Bone Miner Res 2023; 38:1718-1730. [PMID: 37718532 DOI: 10.1002/jbmr.4914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/08/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
SNARE proteins comprise a conserved protein family responsible for catalyzing membrane fusion during vesicle traffic. Syntaxin18 (STX18) is a poorly characterized endoplasmic reticulum (ER)-resident t-SNARE. Recently, together with TANGO1 and SLY1, its involvement was shown in ER to Golgi transport of collagen II during chondrogenesis. We report a fetus with a severe osteochondrodysplasia in whom we identified a homozygous substitution of the highly conserved p.Arg10 to Pro of STX18. CRISPR/Cas9-mediated Stx18 deficiency in zebrafish reveals a crucial role for Stx18 in cartilage and bone development. Furthermore, increased expression of multiple components of the Stx18 SNARE complex and of COPI and COPII proteins suggests that Stx18 deficiency impairs antero- and retrograde vesicular transport in the crispant stx18 zebrafish. Taken together, our studies highlight a new candidate gene for a recessive form of osteochondrodysplasia, thereby possibly broadening the SNAREopathy phenotypic spectrum and opening new doors toward future research avenues. © 2023 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Brecht Guillemyn
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Hanna De Saffel
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Jan Willem Bek
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Piyanoot Tapaneeyaphan
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Adelbert De Clercq
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Tamara Jarayseh
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Sophie Debaenst
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research and Bioimaging Core, Ghent, Belgium
| | - Peter H Byers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
| | - Toon Rosseel
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Paul Coucke
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Bettina Blaumeiser
- Department of Medical Genetics, University and University Hospital of Antwerp, Antwerp, Belgium
| | - Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Sofie Symoens
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
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3
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Stolarova L, Kleiblova P, Zemankova P, Stastna B, Janatova M, Soukupova J, Achatz MI, Ambrosone C, Apostolou P, Arun BK, Auer P, Barnard M, Bertelsen B, Blok MJ, Boddicker N, Brunet J, Burnside ES, Calvello M, Campbell I, Chan SH, Chen F, Chiang JB, Coppa A, Cortesi L, Crujeiras-González A, De Leeneer K, De Putter R, DePersia A, Devereux L, Domchek S, Efremidis A, Engel C, Ernst C, Evans DGR, Feliubadaló L, Fostira F, Fuentes-Ríos O, Gómez-García EB, González S, Haiman C, Hansen TVO, Hauke J, Hodge J, Hu C, Huang H, Ishak NDB, Iwasaki Y, Konstantopoulou I, Kraft P, Lacey J, Lázaro C, Li N, Lim WK, Lindstrom S, Lori A, Martinez E, Martins A, Matsuda K, Matullo G, McInerny S, Michailidou K, Montagna M, Monteiro AN, Mori L, Nathanson K, Neuhausen SL, Nevanlinna H, Olson JE, Palmer J, Pasini B, Patel A, Piane M, Poppe B, Radice P, Renieri A, Resta N, Richardson ME, Rosseel T, Ruddy KJ, Santamariña M, Dos Santos ES, Teras L, Toland AE, Trentham-Dietz A, Vachon CM, Volk AE, Weber-Lassalle N, Weitzel JN, Wiesmuller L, Winham S, Yadav S, Yannoukakos D, Yao S, Zampiga V, Zethoven M, Zhang ZW, Zima T, Spurdle AB, Vega A, Rossing M, Del Valle J, De Nicolo A, Hahnen E, Claes KB, Ngeow J, Momozawa Y, James PA, Couch FJ, Macurek L, Kleibl Z. ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. Clin Cancer Res 2023; 29:3037-3050. [PMID: 37449874 PMCID: PMC10425727 DOI: 10.1158/1078-0432.ccr-23-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). EXPERIMENTAL DESIGN We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. RESULTS A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)-like (N = 226). We then examined their association with breast cancer risk in the case-control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35-3.41), 1.57 (95% CI, 1.41-1.75), and 1.19 (95% CI, 1.08-1.31), respectively. The meta-analysis of population-specific datasets showed similar results. CONCLUSIONS We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.
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Affiliation(s)
- Lenka Stolarova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Stastna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Maria Isabel Achatz
- A.C. Camargo Cancer Center and Oncology Center, Hospital Sirio-Libanes, Sao Paulo, Brazil
| | - Christine Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Cancer Center, Buffalo, New York
- WCHS Inc., Baltimore, Maryland
| | - Paraskevi Apostolou
- Human Molecular Genetics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- WHI, USA
| | - Mollie Barnard
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- CARRIERS, USA
| | - Joan Brunet
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Elizabeth S. Burnside
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
- WWHS, Charlotte, North Carolina
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Ian Campbell
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sock Hoai Chan
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Fei Chen
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Jian Bang Chiang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, Modena University Hospital, Modena, Italy
| | - Ana Crujeiras-González
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robin De Putter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Susan Domchek
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Efremidis
- Clinical Cancer Genetics and Family Consultants, CLINICAGENE, Athens Medical Center, Athens, Greece
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Lidia Feliubadaló
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Olivia Fuentes-Ríos
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Encarna B. Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sara González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - James Hodge
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- CPS3, Kennesaw, Georgia
| | - Chunling Hu
- CARRIERS, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hongyan Huang
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | | | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | - James Lacey
- Beckman Research Institute, City of Hope Cancer Center, Duarte, California
- CTS, USA
| | - Conxi Lázaro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Na Li
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Sara Lindstrom
- WHI, USA
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Adriana Lori
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- American Cancer Society, Atlanta, Georgia
| | - Elana Martinez
- Duke-NUS Medical School, Singapore, Singapore
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, California
| | - Alexandra Martins
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Alvaro N.A. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Luigi Mori
- Endocrine and Metabolic Disease Unit, ASST Spedali Civili of Brescia, Brescia, Italia
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Katherine Nathanson
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Janet E. Olson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- MCBCS, USA
| | - Julie Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Paolo Radice
- Department of Experimental Oncology, Molecular Bases of Genetic Risk and Genetic Testing Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Nicoletta Resta
- Department of Precision and Regenerative Medicine and Ionian Area, Medical Genetics Unit, University of Bari, Bari, Italy
| | | | - Toon Rosseel
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kathryn J. Ruddy
- MCBCS, USA
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Marta Santamariña
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | | | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Amanda E. Toland
- Department of Cancer Biology & Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Amy Trentham-Dietz
- WWHS, Charlotte, North Carolina
- University of Wisconsin, Madison, Wisconsin
| | | | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Lisa Wiesmuller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Stacey Winham
- MMHS, USA
- Department Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Siddhartha Yadav
- CARRIERS, USA
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Song Yao
- WCHS Inc., Baltimore, Maryland
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Magnus Zethoven
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ze Wen Zhang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesús Del Valle
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Joanne Ngeow
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Fergus J. Couch
- CARRIERS, USA
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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4
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Small KW, Van de Sompele S, Nuytemans K, Vincent A, Yuregir OO, Ciloglu E, Sariyildiz C, Rosseel T, Avetisjan J, Udar N, Vance JM, Pericak-Vance MA, De Baere E, Shaya FS. A novel duplication involving PRDM13 in a Turkish family supports its role in North Carolina macular dystrophy (NCMD/MCDR1). Mol Vis 2021; 27:518-527. [PMID: 34526759 PMCID: PMC8410230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Purpose To clinically and molecularly investigate a new family with North Carolina macular dystrophy (NCMD) from Turkey, a previously unreported geographic origin for this phenotype. Methods Clinical ophthalmic examinations, including fundus imaging and spectral domain-optical coherence tomography (SD-OCT), were performed on eight members of a two-generation non-consanguineous family from southern Turkey. Whole genome sequencing (WGS) was performed on two affected subjects, followed by variant filtering and copy number variant (CNV) analysis. Junction PCR and Sanger sequencing were used to confirm and characterize the duplication involving PRDM13 at the nucleotide level. The underlying mechanism was assessed with in silico analyses. Results The proband presented with lifelong bilateral vision impairment and displayed large grade 3 coloboma-like central macular lesions. Five of her six children showed similar macular malformations, consistent with autosomal dominant NCMD. The severity grades in the six affected individuals from two generations are not evenly distributed. CNV analysis of WGS data of the two affected family members, followed by junction PCR and Sanger sequencing, revealed a novel 56.2 kb tandem duplication involving PRDM13 (chr6:99560265-99616492dup, hg38) at the MCDR1 locus. This duplication cosegregates with the NCMD phenotype in the five affected children. No other (likely) pathogenic variants in known inherited retinal disease genes were found in the WGS data. Bioinformatics analyses of the breakpoints suggest a replicative-based repair mechanism underlying the duplication. Conclusions We report a novel tandem duplication involving the PRDM13 gene in a family with NCMD from a previously unreported geographic region. The duplication size is the smallest that has been reported thus far and may correlate with the particular phenotype.
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Affiliation(s)
- Kent W. Small
- Macula and Retina Institute, Glendale and Los Angeles, CA,Molecular Insight Research Foundation, Glendale and Los Angeles, CA
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent Belgium
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Andrea Vincent
- Ophthalmology, New Zealand National Eye Centre, University of Auckland, New Zealand
| | | | - Emine Ciloglu
- University of Health Sciences and Adana City Hospital, Adana, Turkey
| | - Cahfer Sariyildiz
- University of Health Sciences and Adana City Hospital, Adana, Turkey
| | - Toon Rosseel
- Center for Medical Genetics Ghent (CMGG), Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent Belgium
| | - Jessica Avetisjan
- Macula and Retina Institute, Glendale and Los Angeles, CA,Molecular Insight Research Foundation, Glendale and Los Angeles, CA
| | - Nitin Udar
- Macula and Retina Institute, Glendale and Los Angeles, CA,Molecular Insight Research Foundation, Glendale and Los Angeles, CA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL,John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent Belgium
| | - Fadi S. Shaya
- Macula and Retina Institute, Glendale and Los Angeles, CA,Molecular Insight Research Foundation, Glendale and Los Angeles, CA
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5
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Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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6
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Ascari G, Rendtorff ND, De Bruyne M, De Zaeytijd J, Van Lint M, Bauwens M, Van Heetvelde M, Arno G, Jacob J, Creytens D, Van Dorpe J, Van Laethem T, Rosseel T, De Pooter T, De Rijk P, De Coster W, Menten B, Rey AD, Strazisar M, Bertelsen M, Tranebjaerg L, De Baere E. Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss. Front Cell Dev Biol 2021; 9:664317. [PMID: 33968938 PMCID: PMC8097100 DOI: 10.3389/fcell.2021.664317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Inactivating variants as well as a missense variant in the centrosomal CEP78 gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. Apart from this, a complex structural variant (SV) implicating CEP78 has been reported in CRDHL. Here we aimed to expand the genetic architecture of typical CRDHL by the identification of complex SVs of the CEP78 region and characterization of their underlying mechanisms. Approaches used for the identification of the SVs are shallow whole-genome sequencing (sWGS) combined with quantitative polymerase chain reaction (PCR) and long-range PCR, or ExomeDepth analysis on whole-exome sequencing (WES) data. Targeted or whole-genome nanopore long-read sequencing (LRS) was used to delineate breakpoint junctions at the nucleotide level. For all SVs cases, the effect of the SVs on CEP78 expression was assessed using quantitative PCR on patient-derived RNA. Apart from two novel canonical CEP78 splice variants and a frameshifting single-nucleotide variant (SNV), two SVs affecting CEP78 were identified in three unrelated individuals with CRDHL: a heterozygous total gene deletion of 235 kb and a partial gene deletion of 15 kb in a heterozygous and homozygous state, respectively. Assessment of the molecular consequences of the SVs on patient's materials displayed a loss-of-function effect. Delineation and characterization of the 15-kb deletion using targeted LRS revealed the previously described complex CEP78 SV, suggestive of a recurrent genomic rearrangement. A founder haplotype was demonstrated for the latter SV in cases of Belgian and British origin, respectively. The novel 235-kb deletion was delineated using whole-genome LRS. Breakpoint analysis showed microhomology and pointed to a replication-based underlying mechanism. Moreover, data mining of bulk and single-cell human and mouse transcriptional datasets, together with CEP78 immunostaining on human retina, linked the CEP78 expression domain with its phenotypic manifestations. Overall, this study supports that the CEP78 locus is prone to distinct SVs and that SV analysis should be considered in a genetic workup of CRDHL. Finally, it demonstrated the power of sWGS and both targeted and whole-genome LRS in identifying and characterizing complex SVs in patients with ocular diseases.
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Affiliation(s)
- Giulia Ascari
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nanna D Rendtorff
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Michel Van Lint
- Department of Ophthalmology, Antwerp University Hospital, Antwerp, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gavin Arno
- Great Ormond Street Hospital, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom.,UCL Institute of Ophthalmology, London, United Kingdom
| | - Julie Jacob
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mette Bertelsen
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, Glostrup, Denmark
| | - Lisbeth Tranebjaerg
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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7
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Strubbe I, Van Cauwenbergh C, De Zaeytijd J, De Jaegere S, De Bruyne M, Rosseel T, Van de Sompele S, De Baere E, Leroy BP. Phenocopy of a heterozygous carrier of X-linked retinitis pigmentosa due to mosaicism for a RHO variant. Sci Rep 2021; 11:117. [PMID: 33420188 PMCID: PMC7794345 DOI: 10.1038/s41598-020-80400-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
We describe both phenotype and pathogenesis in two male siblings with typical retinitis pigmentosa (RP) and the potentially X-linked RP (XLRP) carrier phenotype in their mother. Two affected sons, two unaffected daughters, and their mother underwent detailed ophthalmological assessments including Goldmann perimetry, color vision testing, multimodal imaging and ISCEV-standard electroretinography. Genetic testing consisted of targeted next-generation sequencing (NGS) of known XLRP genes and whole exome sequencing (WES) of known inherited retinal disease genes (RetNet-WES). Variant validation and segregation analysis were performed by Sanger sequencing. The mutational load of the RHO variant in the mother was assessed in DNA from leucocytes, buccal cells and hair follicles using targeted NGS. Both affected sons showed signs of classical RP, while the mother displayed patches of hyperautofluorescence on blue light autofluorescence imaging and regional, intraretinal, spicular pigmentation, reminiscent of a carrier phenotype of XLRP. XLRP testing was negative. RetNet-WES testing revealed RHO variant c.404G > C p.(Arg135Pro) in a mosaic state (21% of the reads) in the mother and in a heterozygous state in both sons. Targeted NGQSS of the RHO variant in different maternal tissues showed a mutation load between 25.06% and 41.72%. We report for the first time that somatic mosaicism of RHO variant c.404G > C p.(Arg135Pro) mimics the phenotype of a female carrier of XLRP, in combination with heterozygosity for the variant in the two affected sons.
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Affiliation(s)
- Ine Strubbe
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium. .,Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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8
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Ascari G, Peelman F, Farinelli P, Rosseel T, Lambrechts N, Wunderlich KA, Wagner M, Nikopoulos K, Martens P, Balikova I, Derycke L, Holtappels G, Krysko O, Van Laethem T, De Jaegere S, Guillemyn B, De Rycke R, De Bleecker J, Creytens D, Van Dorpe J, Gerris J, Bachert C, Neuhofer C, Walraedt S, Bischoff A, Pedersen LB, Klopstock T, Rivolta C, Leroy BP, De Baere E, Coppieters F. Functional characterization of the first missense variant in CEP78, a founder allele associated with cone-rod dystrophy, hearing loss, and reduced male fertility. Hum Mutat 2020; 41:998-1011. [PMID: 31999394 PMCID: PMC7187288 DOI: 10.1002/humu.23993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Inactivating variants in the centrosomal CEP78 gene have been found in cone-rod dystrophy with hearing loss (CRDHL), a particular phenotype distinct from Usher syndrome. Here, we identified and functionally characterized the first CEP78 missense variant c.449T>C, p.(Leu150Ser) in three CRDHL families. The variant was found in a biallelic state in two Belgian families and in a compound heterozygous state-in trans with c.1462-1G>T-in a third German family. Haplotype reconstruction showed a founder effect. Homology modeling revealed a detrimental effect of p.(Leu150Ser) on protein stability, which was corroborated in patients' fibroblasts. Elongated primary cilia without clear ultrastructural abnormalities in sperm or nasal brushes suggest impaired cilia assembly. Two affected males from different families displayed sperm abnormalities causing infertility. One of these is a heterozygous carrier of a complex allele in SPAG17, a ciliary gene previously associated with autosomal recessive male infertility. Taken together, our data indicate that a missense founder allele in CEP78 underlies the same sensorineural CRDHL phenotype previously associated with inactivating variants. Interestingly, the CEP78 phenotype has been possibly expanded with male infertility. Finally, CEP78 loss-of-function variants may have an underestimated role in misdiagnosed Usher syndrome, with or without sperm abnormalities.
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Affiliation(s)
- Giulia Ascari
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frank Peelman
- Department of Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Toon Rosseel
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Nina Lambrechts
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Kirsten A Wunderlich
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Physiological Genomics, BMC, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Faculty of Medicine, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,Institut für Neurogenomik, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Konstantinos Nikopoulos
- Oncogenomics laboratory, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Pernille Martens
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irina Balikova
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Lara Derycke
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Gabriële Holtappels
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Olga Krysko
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah De Jaegere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Brecht Guillemyn
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,VIB Center for Inflammation Research and BioImaging Core, VIB, Ghent, Belgium
| | - Jan De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jan Gerris
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
| | - Claus Bachert
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Christiane Neuhofer
- Institute of Human Genetics, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Almut Bischoff
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Bart P Leroy
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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9
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Bauwens M, Garanto A, Sangermano R, Naessens S, Weisschuh N, De Zaeytijd J, Khan M, Sadler F, Balikova I, Van Cauwenbergh C, Rosseel T, Bauwens J, De Leeneer K, De Jaegere S, Van Laethem T, De Vries M, Carss K, Arno G, Fakin A, Webster AR, de Ravel de l'Argentière TJL, Sznajer Y, Vuylsteke M, Kohl S, Wissinger B, Cherry T, Collin RWJ, Cremers FPM, Leroy BP, De Baere E. ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel noncoding splice, cis-regulatory, structural, and recurrent hypomorphic variants. Genet Med 2019; 21:1761-1771. [PMID: 30670881 PMCID: PMC6752479 DOI: 10.1038/s41436-018-0420-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Purpose ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Naessens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Françoise Sadler
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jim Bauwens
- Department of Computer Science, Free University of Brussels, Brussels, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Meindert De Vries
- Department of Ophthalmology, Hôpital des Enfants Reine Fabiola, Brussels, Belgium
| | - Keren Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,UK NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Timothy Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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10
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Van Heetvelde M, Van Bockstal M, Poppe B, Lambein K, Rosseel T, Atanesyan L, Deforce D, Van Den Berghe I, De Leeneer K, Van Dorpe J, Vral A, Claes KBM. Accurate detection and quantification of epigenetic and genetic second hits in BRCA1 and BRCA2-associated hereditary breast and ovarian cancer reveals multiple co-acting second hits. Cancer Lett 2018; 425:125-133. [PMID: 29580810 DOI: 10.1016/j.canlet.2018.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/10/2018] [Accepted: 03/16/2018] [Indexed: 10/17/2022]
Abstract
BACKGROUND This study characterizes the second hit spectrum in BRCA1 and BRCA2-associated breast and ovarian cancers at both gene loci to investigate if second hit mechanisms are mutually exclusive or able to coincide within the same tumor. METHODS Loss of heterozygosity, somatic point mutations and copy number alterations along with promoter methylation were studied in 56 breast and 15 ovarian cancers from BRCA1 and BRCA2 germline mutation carriers. A mathematical methodology was introduced to quantify the tumor cell population carrying a second hit. RESULTS Copy neutral LOH was the most prevalent LOH mechanism in this cohort (BC 69%, OC 67%). However, only 36% of BC and 47% of OC showed LOH in all cancerous cells. Somatic intragenic deletions and methylated subclones were also found in combination with (partial) loss of heterozygosity. Unequivocal deleterious somatic point mutations were not identified in this cohort. CONCLUSION Different mechanisms inactivating the wild type allele are present within the same tumor sample at various extents. Results indicate that BRCA1/2-linked breast and ovarian cancer cells are predominantly characterized by LOH, but harbor a complex combination of second hits at various frequencies.
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Affiliation(s)
- Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Basic Medical Sciences, Ghent University, Entrance 46, De Pintelaan 185, B-9000, Ghent, Belgium.
| | - Mieke Van Bockstal
- Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
| | - Bruce Poppe
- Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium.
| | - Kathleen Lambein
- Department of Pathology, AZ St Lucas Hospital, Groenebriel 1, B-9000, Ghent, Belgium; Department of Oncology, KU Leuven, Surgical Oncology, University Hospital Leuven Gasthuisberg, Herestraat 49, O&N1 Box 818, B-3000, Leuven, Belgium.
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
| | - Lilit Atanesyan
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL, Amsterdam, The Netherlands.
| | - Dieter Deforce
- Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
| | - Ivo Van Den Berghe
- Department of Pathology, AZ Sint Jan Hospital Brugge-Oostend, Ruddershove 10, B-8000, Brugge, Belgium.
| | - Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium.
| | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
| | - Anne Vral
- Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Basic Medical Sciences, Ghent University, Entrance 46, De Pintelaan 185, B-9000, Ghent, Belgium.
| | - Kathleen B M Claes
- Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium.
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11
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Baert A, Machackova E, Coene I, Cremin C, Turner K, Portigal-Todd C, Asrat MJ, Nuk J, Mindlin A, Young S, MacMillan A, Van Maerken T, Trbusek M, McKinnon W, Wood ME, Foulkes WD, Santamariña M, de la Hoya M, Foretova L, Poppe B, Vral A, Rosseel T, De Leeneer K, Vega A, Claes KBM. Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11. Hum Mutat 2018; 39:515-526. [PMID: 29280214 DOI: 10.1002/humu.23390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/03/2017] [Accepted: 12/17/2017] [Indexed: 12/31/2022]
Abstract
For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies.
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Affiliation(s)
- Annelot Baert
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ilse Coene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Carol Cremin
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | - Jennifer Nuk
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- BC Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andree MacMillan
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland and Labrador, Canada
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Wendy McKinnon
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - Marie E Wood
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - William D Foulkes
- Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
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12
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Baetens D, Stoop H, Peelman F, Todeschini AL, Rosseel T, Coppieters F, Veitia RA, Looijenga LHJ, De Baere E, Cools M. NR5A1 is a novel disease gene for 46,XX testicular and ovotesticular disorders of sex development. Genet Med 2016; 19:367-376. [PMID: 27490115 PMCID: PMC5392598 DOI: 10.1038/gim.2016.118] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/11/2016] [Indexed: 01/10/2023] Open
Abstract
PURPOSE We aimed to identify the genetic cause in a cohort of 11 unrelated cases and two sisters with 46,XX SRY-negative (ovo)testicular disorders of sex development (DSD). METHODS Whole-exome sequencing (n = 9), targeted resequencing (n = 4), and haplotyping were performed. Immunohistochemistry of sex-specific markers was performed on patients' gonads. The consequences of mutation were investigated using luciferase assays, localization studies, and RNA-seq. RESULTS We identified a novel heterozygous NR5A1 mutation, c.274C>T p.(Arg92Trp), in three unrelated patients. The Arg92 residue is highly conserved and located in the Ftz-F1 region, probably involved in DNA-binding specificity and stability. There were no consistent changes in transcriptional activation or subcellular localization. Transcriptomics in patient-derived lymphocytes showed upregulation of MAMLD1, a direct NR5A1 target previously associated with 46,XY DSD. In gonads of affected individuals, ovarian FOXL2 and testicular SRY-independent SOX9 expression observed. CONCLUSIONS We propose NR5A1, previously associated with 46,XY DSD and 46,XX primary ovarian insufficiency, as a novel gene for 46,XX (ovo)testicular DSD. We hypothesize that p.(Arg92Trp) results in decreased inhibition of the male developmental pathway through downregulation of female antitestis genes, thereby tipping the balance toward testicular differentiation in 46,XX individuals. In conclusion, our study supports a role for NR5A1 in testis differentiation in the XX gonad.Genet Med 19 4, 367-376.
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Affiliation(s)
- Dorien Baetens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Hans Stoop
- Department of Pathology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Peelman
- Flanders Institute for Biotechnology (VIB), Department of Medical Protein Research, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Anne-Laure Todeschini
- Molecular Oncology and Pathology, Institut Jacques Monod, France; Université Paris Diderot, Paris VII, France
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Reiner A Veitia
- Molecular Oncology and Pathology, Institut Jacques Monod, France; Université Paris Diderot, Paris VII, France
| | - Leendert H J Looijenga
- Department of Pathology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Martine Cools
- Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital and Ghent University, Ghent, Belgium
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13
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Dridi M, Rosseel T, Orton R, Johnson P, Lecollinet S, Muylkens B, Lambrecht B, Van Borm S. Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model. J Gen Virol 2015; 96:2999-3009. [PMID: 26297666 DOI: 10.1099/jgv.0.000231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
West Nile virus (WNV) occurs as a population of genetic variants (quasispecies) infecting a single animal. Previous low-resolution viral genetic diversity estimates in sampled wild birds and mosquitoes, and in multiple-passage adaptation studies in vivo or in cell culture, suggest that WNV genetic diversification is mostly limited to the mosquito vector. This study investigated genetic diversification of WNV in avian hosts during a single passage using next-generation sequencing. Wild-captured carrion crows were subcutaneously infected using a clonal Middle-East WNV. Blood samples were collected 2 and 4 days post-infection. A reverse-transcription (RT)-PCR approach was used to amplify the WNV genome directly from serum samples prior to next-generation sequencing resulting in an average depth of at least 700 × in each sample. Appropriate controls were sequenced to discriminate biologically relevant low-frequency variants from experimentally introduced errors. The WNV populations in the wild crows showed significant diversification away from the inoculum virus quasispecies structure. By contrast, WNV populations in intracerebrally infected day-old chickens did not diversify from that of the inoculum. Where previous studies concluded that WNV genetic diversification is only experimentally demonstrated in its permissive insect vector species, we have experimentally shown significant diversification of WNV populations in a wild bird reservoir species.
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Affiliation(s)
- M Dridi
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - T Rosseel
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - R Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - P Johnson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - S Lecollinet
- UMR1161 Virologie INRA, ANSES, ENVA, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 23 avenue du Général De Gaulle, 94706 Maisons-Alfort, France
| | - B Muylkens
- Integrated Veterinary Research Unit, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - B Lambrecht
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - S Van Borm
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
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14
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Rosseel T, Ozhelvaci O, Freimanis G, Van Borm S. Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 2015; 222:72-80. [PMID: 26025457 DOI: 10.1016/j.jviromet.2015.05.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/28/2015] [Accepted: 05/22/2015] [Indexed: 12/27/2022]
Abstract
Viral metagenomic approaches are increasingly being used for viral discovery. Various strategies are applied to enrich viral sequences, but there is often a lack of knowledge about their effective influence on the viral discovery sensitivity. We evaluate some convenient and widely used approaches for RNA virus discovery in clinical samples in order to reveal their sensitivity and potential bias introduced by the enrichment or amplifications steps. An RNA virus was artificially spiked at a fixed titer in serum and lung tissue, respectively, low and high nucleic acid content matrices. For serum, a simple DNase treatment on the RNA extract gave the maximum gain in proportion of viral sequences (83×), and a subsequent ribosomal RNA removal nearly doubled once more the proportion of viral sequences. For lung tissue, a ribosomal RNA depletion step on the RNA extract had the biggest gain in proportion of viral sequences (32×). We show also that direct sequencing of cDNA is recommended above an extra random PCR amplification step, and a that the virion enrichment strategy (filtration and nuclease treatment) has a beneficial effect for sequencing-based virus discovery. Our findings provide sample-dependent guidelines for targeted virus discovery strategies.
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Affiliation(s)
- Toon Rosseel
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Orkun Ozhelvaci
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Graham Freimanis
- The Pirbright Institute, Ash Rd, Woking GU24 0NF, United Kingdom
| | - Steven Van Borm
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium.
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15
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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16
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Rosseel T, Pardon B, De Clercq K, Ozhelvaci O, Van Borm S. False-positive results in metagenomic virus discovery: a strong case for follow-up diagnosis. Transbound Emerg Dis 2014; 61:293-9. [PMID: 24912559 DOI: 10.1111/tbed.12251] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 11/30/2022]
Abstract
A viral metagenomic approach using virion enrichment, random amplification and next-generation sequencing was used to investigate an undiagnosed cluster of dairy cattle presenting with high persistent fever, unresponsive to anti-microbial and anti-inflammatory treatment, diarrhoea and redness of nose and teat. Serum and whole blood samples were taken in the predicted hyperviraemic state of an animal that a few days later presented with these clinical signs. Bioinformatics analysis of the resulting data from the DNA virus identification workflow (a total of 32 757 sequences with average read length 335 bases) initially demonstrated the presence of parvovirus-like sequences in the tested blood sample. Thorough follow-up using specific real-time RT-PCR assays targeting the detected sequence fragments confirmed the presence of these sequences in the original sample as well as in a sample of an additional animal, but a contamination with an identical genetic signature in negative extraction controls was demonstrated. Further investigation using an alternative extraction method identified a contamination of the originally used Qiagen extraction columns with parvovirus-like nucleic acids or virus particles. Although we did not find any relevant virus that could be associated with the disease, these observations clearly illustrate the importance of using a proper control strategy and follow-up diagnostic tests in any viral metagenomic study.
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Affiliation(s)
- T Rosseel
- Veterinary and Agrochemical Research Centre, Department of Virology, Molecular Platform Unit, Ukkel, Belgium
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Vandenbussche F, Sailleau C, Rosseel T, Desprat A, Viarouge C, Richardson J, Eschbaumer M, Hoffmann B, De Clercq K, Bréard E, Zientara S. Full-Genome Sequencing of Four Bluetongue Virus Serotype 11 Viruses. Transbound Emerg Dis 2013; 62:565-71. [PMID: 24750582 DOI: 10.1111/tbed.12178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Indexed: 11/29/2022]
Abstract
Recently, a contamination incident was described in which the challenge inoculum used in a bluetongue virus serotype 8 (BTV-8) vaccination trial was contaminated with a BTV-11 virus that was closely related to the Belgian BTV-11 virus from 2008. This study reports the first complete genome sequences of four BTV-11 viruses: the BTV-11 contaminant, BTV-11 reference strain, BTV-11 vaccine strain and a recently isolated BTV-11 field strain from Martinique. Full-genome analysis showed that these viruses belong to serotype 11/nucleotype A and cluster together with other western topotype bluetongue viruses. Detailed comparisons of the genomes further indicated that the contaminant was derived from the BTV-11 reference strain, as they were distinguished by a single synonymous nucleotide substitution. The previously reported partial sequence of genome segment 2 of the Belgian BTV-11 was found to be identical to that of the BTV-11 vaccine strain, indicating that it most likely was the BTV-11 vaccine strain. These findings also suggest that the BTV-11 contaminant and the Belgian BTV-11 are not the same viruses. Finally, comparison of the reference and vaccine strain did not allow determining the amino acid substitutions that contribute to the attenuated phenotype.
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Affiliation(s)
- F Vandenbussche
- Operational Directorate of Viral Diseases, Molecular Platform, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - C Sailleau
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - T Rosseel
- Operational Directorate of Viral Diseases, Molecular Platform, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - A Desprat
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - C Viarouge
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - J Richardson
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - M Eschbaumer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - B Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - K De Clercq
- Operational Directorate of Viral Diseases, Vesicular and Exotic Diseases, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - E Bréard
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - S Zientara
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
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Van Borm S, Rosseel T, Vangeluwe D, Vandenbussche F, van den Berg T, Lambrecht B. Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls. Arch Virol 2012; 157:1509-22. [PMID: 22580556 DOI: 10.1007/s00705-012-1323-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/22/2012] [Indexed: 11/28/2022]
Abstract
Nine influenza viruses isolated from gulls and shorebirds in Belgium (2008-2010), including H3N8, H5N2, H6N1, H11N9, H13N6, H13N8, and H16N3 subtypes, were targeted using random amplification and next-generation sequencing. The gene segments of these viruses segregated into three phylogeographic lineage types: (1) segments circulating in waterfowl in Eurasia with sporadic introduction in other species and in the Americas ("Eurasian avian"), (2) segments circulating in American waterfowl with sporadic introduction to other species and regions ("American avian"), and (3) segments circulating exclusively in gulls and shorebirds and having increased connectivity between the two hemispheres ("Charadriiformes specific"). Notably, an H6N1 and an H5N2 isolated from L. argentatus had mainly Eurasian avian genes but shared a matrix segment of American avian origin (first documentation in European gulls of transhemispheric reassortment). These data support the growing evidence of an important role of Charadriiformes birds in the dynamic nature of avian influenza ecology.
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Affiliation(s)
- Steven Van Borm
- Department of Virology, Veterinary and Agrochemical Research Center, Groeselenbergstraat 99, 1180 Uccle, Belgium.
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Rosseel T, Lambrecht B, Vandenbussche F, van den Berg T, Van Borm S. Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies. Virol J 2011; 8:463. [PMID: 21978491 PMCID: PMC3219605 DOI: 10.1186/1743-422x-8-463] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/06/2011] [Indexed: 02/05/2023] Open
Abstract
Background During a wildlife screening program for avian influenza A viruses (AIV) and avian paramyxoviruses (APMV) in Belgium, we isolated two hemagglutinating agents from pools of cloacal swabs of wild mallards (Anas platyrhynchos) caught in a single sampling site at two different times. AIV and APMV1 were excluded using hemagglutination inhibition (HI) testing and specific real-time RT-PCR tests. Methods To refine the virological identification of APMV2-10 realized by HI subtyping tests and in lack of validated molecular tests for APMV2-10, random access amplification was used in combination with next generation sequencing for the sequence independent identification of the viruses and the determination of their genomes. Results Three different APMVs were identified. From one pooled sample, the complete genome sequence (15054 nucleotides) of an APMV4 was assembled from the random sequences. From the second pooled sample, the nearly complete genome sequence of an APMV6 (genome size of 16236 nucleotides) was determined, as well as a partial sequence for an APMV4. This APMV4 was closely related but not identical to the APMV4 isolated from the first sample. Although a cross-reactivity with other APMV subtypes did not allow formal identification, the HI subtyping revealed APMV4 and APMV6 in the respective pooled samples but failed to identify the co-infecting APMV4 in the APMV6 infected pool. Conclusions These data further contribute to the knowledge about the genetic diversity within the serotypes APMV4 and 6, and confirm the limited sensitivity of the HI subtyping test. Moreover, this study demonstrates the value of a random access nucleic acid amplification method in combination with massive parallel sequencing. Using only a moderate and economical sequencing effort, the characterization and full genome sequencing of APMVs can be obtained, including the identification of viruses in mixed infections.
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Affiliation(s)
- Toon Rosseel
- Operational Directorate of Virology, Veterinary and Agrochemical Research Center, Ukkel, Belgium
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Datz S, Hippler R, Andersen LH, Dittner PF, Knudsen H, Krause HF, Miller PD, Pepmiller PL, Rosseel T, Schuch R, Stolterfoht N, Yamazaki Y, Vane CR. Coincidence studies of capture and ionization in highly charged Iq+-He and Uq+-He collisions at medium velocities. Phys Rev A 1990; 41:3559-3571. [PMID: 9903526 DOI: 10.1103/physreva.41.3559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Anteunis M, Verhegghe G, Rosseel T. Configurational and conformational insights onexo- anden do-1, 4:3, 6-dianhydroglucitol mononitrate. ACTA ACUST UNITED AC 1971. [DOI: 10.1002/mrc.1270030608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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