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Haer-Wigman L, den Ouden A, Derks R, van Genderen MM, Lugtenberg D, Verheij J, Vijzelaar R, Yntema HG, Vissers LELM, Neveling K. Reply to: Pitfalls in the genetic testing of the OPN1LW-OPN1MW gene cluster in human subjects. NPJ Genom Med 2024; 9:29. [PMID: 38704388 PMCID: PMC11069539 DOI: 10.1038/s41525-024-00409-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/13/2024] [Indexed: 05/06/2024] Open
Affiliation(s)
- Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Amber den Ouden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria M van Genderen
- Bartiméus Diagnostic Center for complex visual disorders, Zeist, the Netherlands
- Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joke Verheij
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
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Levy B, Kanagal-Shamanna R, Sahajpal NS, Neveling K, Rack K, Dewaele B, Olde Weghuis D, Stevens-Kroef M, Puiggros A, Mallo M, Clifford B, Mantere T, Hoischen A, Espinet B, Kolhe R, Solé F, Raca G, Smith AC. A framework for the clinical implementation of optical genome mapping in hematologic malignancies. Am J Hematol 2024; 99:642-661. [PMID: 38164980 DOI: 10.1002/ajh.27175] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/12/2023] [Revised: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Mallo
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Francesc Solé
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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3
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Marouane A, Neveling K, Deden AC, van den Heuvel S, Zafeiropoulou D, Castelein S, van de Veerdonk F, Koolen DA, Simons A, Rodenburg R, Westra D, Mensenkamp AR, de Leeuw N, Ligtenberg M, Matthijsse R, Pfundt R, Kamsteeg EJ, Brunner HG, Gilissen C, Feenstra I, de Boode WP, Yntema HG, van Zelst-Stams WAG, Nelen M, Vissers LELM. Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease. Front Genet 2024; 14:1304520. [PMID: 38259611 PMCID: PMC10800954 DOI: 10.3389/fgene.2023.1304520] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Rapid exome sequencing (rES) has become the first-choice genetic test for critically ill patients, mostly neonates, young infants, or fetuses in prenatal care, in time-sensitive situations and when it is expected that the genetic test result may guide clinical decision making. The implementation of rES has revolutionized medicine by enabling timely identification of genetic causes for various rare diseases. The utilization of rES has increasingly been recognized as an essential diagnostic tool for the identification of complex and undiagnosed genetic disorders. Methods: We conducted a retrospective evaluation of our experiences with rES performed on 575 critically ill patients from various age groups (prenatal to adulthood), over a four-year period (2016-2019). These patients presented with a wide spectrum of rare diseases, including but not limited to neurological disorders, severe combined immune deficiency, and cancer. Results: During the study period, there was a significant increase in rES referrals, with a rise from a total of two referrals in Q1-2016 to 10 referrals per week in Q4-2019. The median turnaround time (TAT) decreased from 17 to 11 days in the period 2016-2019, with an overall median TAT of 11 days (IQR 8-15 days). The overall diagnostic yield for this cohort was 30.4%, and did not significantly differ between the different age groups (e.g. adults 22.2% vs children 31.0%; p-value 0.35). However, variability in yield was observed between clinical entities: craniofacial anomalies yielded 58.3%, while for three clinical entities (severe combined immune deficiency, aneurysm, and hypogonadotropic hypogonadism) no diagnoses were obtained. Discussion: Importantly, whereas clinical significance is often only attributed to a conclusive diagnosis, we also observed impact on clinical decision-making for individuals in whom no genetic diagnosis was established. Hence, our experience shows that rES has an important role for patients of all ages and across the broad spectrum of rare diseases to impact clinical outcomes.
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Affiliation(s)
- Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - A. Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - David A. Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Richard Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dineke Westra
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marjolijn Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rene Matthijsse
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem P. de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
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4
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de Boer E, Marcelis C, Neveling K, van Beusekom E, Hoischen A, Klein WM, de Leeuw N, Mantere T, Melo US, van Reeuwijk J, Smeets D, Spielmann M, Kleefstra T, van Bokhoven H, Vissers LE. A complex structural variant near SOX3 causes X-linked split-hand/foot malformation. HGG Adv 2023; 4:100200. [PMID: 37216008 PMCID: PMC10196709 DOI: 10.1016/j.xhgg.2023.100200] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Split-hand/foot malformation (SHFM) is a congenital limb defect most typically presenting with median clefts in hands and/or feet, that can occur in a syndromic context as well as in isolated form. SHFM is caused by failure to maintain normal apical ectodermal ridge function during limb development. Although several genes and contiguous gene syndromes are implicated in the monogenic etiology of isolated SHFM, the disorder remains genetically unexplained for many families and associated genetic loci. We describe a family with isolated X-linked SHFM, for which the causative variant could be detected after a diagnostic journey of 20 years. We combined well-established approaches including microarray-based copy number variant analysis and fluorescence in situ hybridization coupled with optical genome mapping and whole genome sequencing. This strategy identified a complex structural variant (SV) comprising a 165-kb gain of 15q26.3 material ([GRCh37/hg19] chr15:99795320-99960362dup) inserted in inverted position at the site of a 38-kb deletion on Xq27.1 ([GRCh37/hg19] chrX:139481061-139518989del). In silico analysis suggested that the SV disrupts the regulatory framework on the X chromosome and may lead to SOX3 misexpression. We hypothesize that SOX3 dysregulation in the developing limb disturbed the fine balance between morphogens required for maintaining AER function, resulting in SHFM in this family.
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Affiliation(s)
- Elke de Boer
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Ellen van Beusekom
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willemijn M. Klein
- Department of Medical Imaging, Radiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Uirá S. Melo
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, 23562 Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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de Bruijn SE, Rodenburg K, Corominas J, Ben-Yosef T, Reurink J, Kremer H, Whelan L, Plomp AS, Berger W, Farrar GJ, Ferenc Kovács Á, Fajardy I, Hitti-Malin RJ, Weisschuh N, Weener ME, Sharon D, Pennings RJE, Haer-Wigman L, Hoyng CB, Nelen MR, Vissers LELM, van den Born LI, Gilissen C, Cremers FPM, Hoischen A, Neveling K, Roosing S. Optical genome mapping and revisiting short-read genome sequencing data reveal previously overlooked structural variants disrupting retinal disease-associated genes. Genet Med 2023; 25:100345. [PMID: 36524988 DOI: 10.1016/j.gim.2022.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 07/19/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Structural variants (SVs) play an important role in inherited retinal diseases (IRD). Although the identification of SVs significantly improved upon the availability of genome sequencing, it is expected that involvement of SVs in IRDs is higher than anticipated. We revisited short-read genome sequencing data to enhance the identification of gene-disruptive SVs. METHODS Optical genome mapping was performed to improve SV detection in short-read genome sequencing-negative cases. In addition, reanalysis of short-read genome sequencing data was performed to improve the interpretation of SVs and to re-establish SV prioritization criteria. RESULTS In a monoallelic USH2A case, optical genome mapping identified a pericentric inversion (173 megabase), with 1 breakpoint disrupting USH2A. Retrospectively, the variant could be observed in genome sequencing data but was previously deemed false positive. Reanalysis of short-read genome sequencing data (427 IRD cases) was performed which yielded 30 pathogenic SVs affecting, among other genes, USH2A (n = 15), PRPF31 (n = 3), and EYS (n = 2). Eight of these (>25%) were overlooked during previous analyses. CONCLUSION Critical evaluation of our findings allowed us to re-establish and improve our SV prioritization and interpretation guidelines, which will prevent missing pathogenic events in future analyses. Our data suggest that more attention should be paid to SV interpretation and the current contribution of SVs in IRDs is still underestimated.
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Affiliation(s)
- Suzanne E de Bruijn
- 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.
| | - Kim Rodenburg
- 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
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Janine Reurink
- 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
| | - Hannie Kremer
- 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; Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura Whelan
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland; Neuroscience Center Zurich (ZNZ), University and ETH Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Árpád Ferenc Kovács
- 2nd Department of Paediatrics, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Isabelle Fajardy
- Division of Maternal Malnutrition, Department of Perinatal Environment and Health, Lille University, Lille, France; Division Biochemistry and Molecular Biology, Biology and Pathology Center, Lille, France
| | - Rebekkah J Hitti-Malin
- 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
| | - Nicole Weisschuh
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronald J E Pennings
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- 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
| | | | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, 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
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- 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
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6
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Averdunk L, Huetzen MA, Moreno-Andrés D, Kalb R, McKee S, Hsieh TC, Seibt A, Schouwink M, Lalani S, Faqeih EA, Brunet T, Boor P, Neveling K, Hoischen A, Hildebrandt B, Graf E, Lu L, Jin W, Schaper J, Omer JA, Demaret T, Fleischer N, Schindler D, Krawitz P, Mayatepek E, Wieczorek D, Wang LL, Antonin W, Jachimowicz RD, von Felbert V, Distelmaier F. Biallelic variants in CRIPT cause a Rothmund-Thomson-like syndrome with increased cellular senescence. Genet Med 2023:100836. [PMID: 37013901 DOI: 10.1016/j.gim.2023.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
PURPOSE Rothmund-Thomson syndrome (RTS) is characterized by poikiloderma, sparse hair, small stature, skeletal defects, cancer, cataracts, resembling features of premature aging. RECQL4 and ANAPC1 are the two known disease genes associated with RTS in over 70% of cases. We describe RTS-like features in five individuals with biallelic variants in CRIPT (OMIM#615789). METHODS Two newly identified and four published individuals with CRIPT variants were systematically compared to RTS using clinical data, computational analysis of photographs, histologic analysis of skin, and cellular studies on fibroblasts. RESULTS All CRIPT individuals fulfilled the diagnostic criteria for RTS, and additionally had neurodevelopmental delay and seizures. Using computational gestalt analysis, CRIPT individuals showed greatest facial similarity with RTS individuals. Skin biopsies revealed a high expression of senescence markers (p53/p16/p21) and the senescence-associated ß-galactosidase activity was elevated in CRIPT-deficient fibroblasts. RECQL4- and CRIPT-deficient fibroblasts showed an unremarkable mitotic progression and unremarkable number of mitotic errors, and no or only mild sensitivity to genotoxic stress by ionizing radiation, mitomycin C, hydroxyurea, etoposide, and potassium bromate. CONCLUSION CRIPT causes an RTS-like syndrome associated with neurodevelopmental delay and epilepsy. At the cellular level, RECQL4- and CRIPT-deficient cells display increased senescence, suggesting shared molecular mechanisms leading to the clinical phenotypes.
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7
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Viering DH, Hureaux M, Neveling K, Latta F, Kwint M, Blanchard A, Konrad M, Bindels RJ, Schlingmann KP, Vargas-Poussou R, de Baaij JH. Long-Read Sequencing Identifies Novel Pathogenic Intronic Variants in Gitelman Syndrome. J Am Soc Nephrol 2023; 34:333-345. [PMID: 36302598 PMCID: PMC10103101 DOI: 10.1681/asn.2022050627] [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] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gitelman syndrome is a salt-losing tubulopathy characterized by hypokalemic alkalosis and hypomagnesemia. It is caused by homozygous recessive or compound heterozygous pathogenic variants in SLC12A3 , which encodes the Na + -Cl - cotransporter (NCC). In up to 10% of patients with Gitelman syndrome, current genetic techniques detect only one specific pathogenic variant. This study aimed to identify a second pathogenic variant in introns, splice sites, or promoters to increase the diagnostic yield. METHODS Long-read sequencing of SLC12A3 was performed in 67 DNA samples from individuals with suspected Gitelman syndrome in whom a single likely pathogenic or pathogenic variant was previously detected. In addition, we sequenced DNA samples from 28 individuals with one variant of uncertain significance or no candidate variant. Midigene splice assays assessed the pathogenicity of novel intronic variants. RESULTS A second likely pathogenic/pathogenic variant was identified in 45 (67%) patients. Those with two likely pathogenic/pathogenic variants had a more severe electrolyte phenotype than other patients. Of the 45 patients, 16 had intronic variants outside of canonic splice sites (nine variants, mostly deep intronic, six novel), whereas 29 patients had an exonic variant or canonic splice site variant. Midigene splice assays of the previously known c.1670-191C>T variant and intronic candidate variants demonstrated aberrant splicing patterns. CONCLUSION Intronic pathogenic variants explain an important part of the missing heritability in Gitelman syndrome. Long-read sequencing should be considered in diagnostic workflows for Gitelman syndrome.
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Affiliation(s)
- Daan H.H.M. Viering
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marguerite Hureaux
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Paris CardioVascular Research Center, Institut National de la Santé et de Recherche Médicale (INSERM) U970, Paris City University, Paris, France
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Femke Latta
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anne Blanchard
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, University of Paris, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Martin Konrad
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - René J.M. Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Rosa Vargas-Poussou
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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8
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Lassche G, van Engen-van Grunsven ACH, van Hooij O, Aalders TW, Am Weijers J, Cocco E, Drilon A, Hoischen A, Neveling K, Schalken JA, Verhaegh GW, van Herpen CML. Precision oncology using organoids of a secretory carcinoma of the salivary gland treated with TRK-inhibitors. Oral Oncol 2023; 137:106297. [PMID: 36610231 PMCID: PMC10360362 DOI: 10.1016/j.oraloncology.2022.106297] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
The use of anticancer drugs targeting specific molecular tumor characteristics is rapidly increasing in clinical practice, but selecting patients to benefit from these remains a challenge. It has been suggested that organoid cultures would be ideally suited to test drug responses in vitro. Here we describe and characterize in depth a case of ETV6-NTRK3 gene fusion-positive secretory carcinoma of the salivary glands and corresponding organoid cultures that responded and subsequently acquired resistance to TRK targeting therapy with larotrectinib. This case-culture-characterization illustrates the advances made in precision oncology, but also exposes important caveats in using organoids to predict treatment response.
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Affiliation(s)
- Gerben Lassche
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Adriana C H van Engen-van Grunsven
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands; Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Onno van Hooij
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Tilly W Aalders
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Jetty Am Weijers
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Emiliano Cocco
- University of Miami, Miller School of Medicine, Department of Biochemistry and Molecular Biology/Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Alexander Hoischen
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands; Radboud university medical center, Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands; Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud university medical center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jack A Schalken
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Carla M L van Herpen
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.
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9
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Te Paske IBAW, Mensenkamp AR, Neveling K, Hoogerbrugge N, Ligtenberg MJL, De Voer RM. Noncoding Aberrations in Mismatch Repair Genes Underlie a Substantial Part of the Missing Heritability in Lynch Syndrome. Gastroenterology 2022; 163:1691-1694.e7. [PMID: 36037994 DOI: 10.1053/j.gastro.2022.08.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Iris B A W Te Paske
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | | | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Department of Pathology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Richarda M De Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.
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10
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Haer-Wigman L, den Ouden A, van Genderen MM, Kroes HY, Verheij J, Smailhodzic D, Hoekstra AS, Vijzelaar R, Blom J, Derks R, Tjon-Pon-Fong M, Yntema HG, Nelen MR, Vissers LELM, Lugtenberg D, Neveling K. Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA. NPJ Genom Med 2022; 7:65. [PMID: 36351915 PMCID: PMC9646815 DOI: 10.1038/s41525-022-00334-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
Pathogenic variants in the OPN1LW/OPN1MW gene cluster are causal for a range of mild to severe visual impairments with color deficiencies. The widely utilized short-read next-generation sequencing (NGS) is inappropriate for the analysis of the OPN1LW/OPN1MW gene cluster and many patients with pathogenic variants stay underdiagnosed. A diagnostic genetic assay was developed for the OPN1LW/OPN1MW gene cluster, consisting of copy number analysis via multiplex ligation-dependent probe amplification and sequence analysis via long-read circular consensus sequencing. Performance was determined on 50 clinical samples referred for genetic confirmation of the clinical diagnosis (n = 43) or carrier status analysis (n = 7). A broad range of pathogenic haplotypes were detected, including deletions, hybrid genes, single variants and combinations of variants. The developed genetic assay for the OPN1LW/OPN1MW gene cluster is a diagnostic test that can detect both structural and nucleotide variants with a straightforward analysis, improving diagnostic care of patients with visual impairment.
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Affiliation(s)
- Lonneke Haer-Wigman
- 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.
| | - Amber den Ouden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria M van Genderen
- Bartiméus Diagnostic Center for complex visual disorders, Zeist, The Netherlands
- Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joke Verheij
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dzenita Smailhodzic
- Bartiméus Diagnostic Center for complex visual disorders, Zeist, The Netherlands
- The Rotterdam Eye Hospital, Rotterdam, 3011 BH, The Netherlands
| | | | | | - Jan Blom
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Menno Tjon-Pon-Fong
- 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
| | - Helger G Yntema
- 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
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- 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
| | - Dorien Lugtenberg
- 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
| | - Kornelia Neveling
- 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
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11
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Smith A, Kanagal-Shamanna R, Dewaele B, Rack K, Hoischen A, Neveling K, Raca G, Levy B, Kolhe R, Espinet B, Puiggros A, Sole F, Mallo M. 16. International working group recommendations for the implementation of optical genome mapping in Hematologic Malignancies. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Smith AC, Neveling K, Kanagal‐Shamanna R. Optical genome mapping for structural variation analysis in hematologic malignancies. Am J Hematol 2022; 97:975-982. [PMID: 35560245 DOI: 10.1002/ajh.26587] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/19/2022]
Abstract
Optical genome mapping (OGM) is a technology that is rapidly being adopted in clinical genetics laboratories for its ability to detect structural variation (e.g., translocations, inversions, deletions, duplications, etc.) and replace several concurrent standard of care techniques (karyotype, fluorescence in situ hybridization, and chromosomal microarray). OGM can dramatically simplify lab workflow by reducing multiple tests (conventional karyotype, fluorescence in situ hybridization [FISH], and chromosomal microarray) into one test. The superior ability to detect structural variation across the genome removes the need for reflex FISH studies, which can dramatically reduce cost and turnaround time per sample. Parallel studies of OGM versus standard of care testing have demonstrated it can detect and resolve more abnormalities than karyotyping or FISH. However, like many molecular tests that normalize copy number it can have difficulty with non-diploid karyotypes. This Test of the Month review will summarize how the technique works, review the strengths and weaknesses of OGM compared to standard of care techniques and illustrate how the technique is likely to change front line testing in many hematologic malignancies-including summarizing the clinical utility in acute myeloid leukemia, myelodysplastic syndromes, and B cell acute lymphoblastic leukemia.
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Affiliation(s)
- Adam C. Smith
- Laboratory Medicine Program University Health Network Toronto Ontario Canada
- The Department of Laboratory Medicine and Pathobiology, Faculty of Medicine University of Toronto Toronto Ontario Canada
| | - Kornelia Neveling
- Department of Human Genetics Radboud University Medical Center Nijmegen the Netherlands
| | - Rashmi Kanagal‐Shamanna
- Department of Hematopathology and Molecular Diagnostics The University of Texas MD Anderson Cancer Center Houston Texas USA
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13
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Smits JJ, de Bruijn SE, Lanting CP, Oostrik J, O'Gorman L, Mantere T, Cremers FPM, Roosing S, Yntema HG, de Vrieze E, Derks R, Hoischen A, Pegge SAH, Neveling K, Pennings RJE, Kremer H. Correction to: Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. Hum Genet 2021; 141:991. [PMID: 34608567 DOI: 10.1007/s00439-021-02377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sjoert A H Pegge
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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14
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Smits JJ, de Bruijn SE, Lanting CP, Oostrik J, O'Gorman L, Mantere T, Cremers FPM, Roosing S, Yntema HG, de Vrieze E, Derks R, Hoischen A, Pegge SAH, Neveling K, Pennings RJE, Kremer H. Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. Hum Genet 2021; 141:465-484. [PMID: 34410491 PMCID: PMC9035008 DOI: 10.1007/s00439-021-02336-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.
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Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sjoert A H Pegge
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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15
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Mantere T, Neveling K, Pebrel-Richard C, Benoist M, van der Zande G, Kater-Baats E, Baatout I, van Beek R, Yammine T, Oorsprong M, Hsoumi F, Olde-Weghuis D, Majdali W, Vermeulen S, Pauper M, Lebbar A, Stevens-Kroef M, Sanlaville D, Dupont JM, Smeets D, Hoischen A, Schluth-Bolard C, El Khattabi L. Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet 2021; 108:1409-1422. [PMID: 34237280 PMCID: PMC8387289 DOI: 10.1016/j.ajhg.2021.05.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [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: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Céline Pebrel-Richard
- Department of Chromosomal and Molecular Genetics, University Hospital of Clermont-Ferrand, 63003 Clermont-Ferrand, France
| | - Marion Benoist
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Imane Baatout
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Tony Yammine
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Unit of Medical Genetics, Saint-Joseph University, 1107 2180 Beyrouth, Lebanon
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Faten Hsoumi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Daniel Olde-Weghuis
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Wed Majdali
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Aziza Lebbar
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Damien Sanlaville
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Jean Michel Dupont
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
| | - Caroline Schluth-Bolard
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Laïla El Khattabi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France.
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16
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Neveling K, Mantere T, Vermeulen S, Oorsprong M, van Beek R, Kater-Baats E, Pauper M, van der Zande G, Smeets D, Weghuis DO, Stevens-Kroef MJPL, Hoischen A. Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping. Am J Hum Genet 2021; 108:1423-1435. [PMID: 34237281 DOI: 10.1016/j.ajhg.2021.06.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [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: 10/01/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Somatic structural variants (SVs) are important drivers of cancer development and progression. In a diagnostic set-up, especially for hematological malignancies, the comprehensive analysis of all SVs in a given sample still requires a combination of cytogenetic techniques, including karyotyping, FISH, and CNV microarrays. We hypothesize that the combination of these classical approaches could be replaced by optical genome mapping (OGM). Samples from 52 individuals with a clinical diagnosis of a hematological malignancy, divided into simple (<5 aberrations, n = 36) and complex (≥5 aberrations, n = 16) cases, were processed for OGM, reaching on average: 283-fold genome coverage. OGM called a total of 918 high-confidence SVs per sample, of which, on average, 13 were rare and >100 kb. In addition, on average, 73 CNVs were called per sample, of which six were >5 Mb. For the 36 simple cases, all clinically reported aberrations were detected, including deletions, insertions, inversions, aneuploidies, and translocations. For the 16 complex cases, results were largely concordant between standard-of-care and OGM, but OGM often revealed higher complexity than previously recognized. Detailed technical comparison with standard-of-care tests showed high analytical validity of OGM, resulting in a sensitivity of 100% and a positive predictive value of >80%. Importantly, OGM resulted in a more complete assessment than any previous single test and most likely reported the most accurate underlying genomic architecture (e.g., for complex translocations, chromoanagenesis, and marker chromosomes). In conclusion, the excellent concordance of OGM with diagnostic standard assays demonstrates its potential to replace classical cytogenetic tests as well as to rapidly map novel leukemia drivers.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6532 GA Nijmegen, the Netherlands.
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17
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Sabatella M, Mantere T, Waanders E, Neveling K, Mensenkamp AR, van Dijk F, Hehir‐Kwa JY, Derks R, Kwint M, O'Gorman L, Tropa Martins M, Gidding CEM, Lequin MH, Küsters B, Wesseling P, Nelen M, Biegel JA, Hoischen A, Jongmans MC, Kuiper RP. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol 2021; 255:202-211. [PMID: 34231212 PMCID: PMC8519051 DOI: 10.1002/path.5755] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat‐rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long‐range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE‐VNTR‐Alu, subfamily E (SVA‐E) retrotransposon element, which was present in a mosaic state in the mother. This SVA‐E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long‐read sequencing to identify genomic variations in high‐risk cancer‐predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Tuomo Mantere
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter OuluUniversity of OuluOuluFinland
| | - Esmé Waanders
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Kornelia Neveling
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Arjen R Mensenkamp
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Freerk van Dijk
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
| | | | - Ronnie Derks
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Michael Kwint
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Luke O'Gorman
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | | | - Maarten H Lequin
- Department of RadiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Benno Küsters
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Pieter Wesseling
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of PathologyAmsterdam University Medical Centers, Location VUmc and Brain Tumor Center AmsterdamAmsterdamThe Netherlands
| | - Marcel Nelen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Jacklyn A Biegel
- Department of Pathology and Laboratory MedicineChildren's Hospital, Los AngelesLos AngelesCAUSA
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI)Radboud University Medical CenterNijmegenThe Netherlands
| | - Marjolijn C Jongmans
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Roland P Kuiper
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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18
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Coolen JPM, den Drijver EPM, Verweij JJ, Schildkraut JA, Neveling K, Melchers WJG, Kolwijck E, Wertheim HFL, Kluytmans JAJW, Huynen MA. Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance. Microb Genom 2021; 7:000556. [PMID: 33843573 PMCID: PMC8208684 DOI: 10.1099/mgen.0.000556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harbouring antibiotic-resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosome-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to CTX resistance has not been reported. We recultured 172 cefoxitin-resistant E. coli isolates with known CTX minimum inhibitory concentrations and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio sequenced reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a T at the -42 position rather than the wild-type C, resulted from 18 independent C>T mutations in five phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (false discovery rate <0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underlines the role of recurrent mutations in the spread of antibiotic resistance.
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Affiliation(s)
- Jordy P. M. Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evert P. M. den Drijver
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jaco J. Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jodie A. Schildkraut
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva Kolwijck
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan A. J. W. Kluytmans
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Microbiology, Microvida, Breda, The Netherlands
- Julius Center for Health Sciences and Primary Care, UMCU, Utrecht, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
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de Vrieze E, Cañas Martín J, Peijnenborg J, Martens A, Oostrik J, van den Heuvel S, Neveling K, Pennings R, Kremer H, van Wijk E. AON-based degradation of c.151C>T mutant COCH transcripts associated with dominantly inherited hearing impairment DFNA9. Mol Ther Nucleic Acids 2021; 24:274-283. [PMID: 33815940 PMCID: PMC7985667 DOI: 10.1016/j.omtn.2021.02.033] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
The c.151C>T founder mutation in COCH is a frequent cause of late-onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutant COCH transcripts has high therapeutic potential. Single-molecule real-time (SMRT) sequencing resulted in the identification of 11 variants with a low population frequency (<10%) that are specific to the c.151C>T mutant COCH allele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to induce mutant COCH transcript degradation when delivered to transgenic cells expressing COCH minigenes. The most potent AON, directed against the c.151C>T mutation, was able to induce a 60% decrease in mutant COCH transcripts without affecting wild-type COCH transcript levels. Allele specificity decreased when increasing concentrations of AON were delivered to the cells. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
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Affiliation(s)
- Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author: Erik de Vrieze, Department of Otorhinolaryngology, Radboud University Medical Center, P.O. Box 9101, 6525 GA Nijmegen (Route 855), the Netherlands.
| | - Jorge Cañas Martín
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jolien Peijnenborg
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Aniek Martens
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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20
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Deden C, Neveling K, Zafeiropopoulou D, Gilissen C, Pfundt R, Rinne T, de Leeuw N, Faas B, Gardeitchik T, Sallevelt SCEH, Paulussen A, Stevens SJC, Sikkel E, Elting MW, van Maarle MC, Diderich KEM, Corsten-Janssen N, Lichtenbelt KD, Lachmeijer G, Vissers LELM, Yntema HG, Nelen M, Feenstra I, van Zelst-Stams WAG. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging. Prenat Diagn 2020; 40:972-983. [PMID: 32333414 PMCID: PMC7497059 DOI: 10.1002/pd.5717] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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: 12/23/2019] [Revised: 03/01/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Objective The purpose of this study was to explore the diagnostic yield and clinical utility of trio‐based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging. Methods In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7). Results A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases. Conclusions These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.
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Affiliation(s)
- Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Dimitra Zafeiropopoulou
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Brigitte Faas
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Aimee Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Esther Sikkel
- Department of Obstetrics and Gynecology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Mariet W Elting
- Department of Clinical Genetics, AMsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Merel C van Maarle
- Department of Clinical Genetics, AMsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Klaske D Lichtenbelt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Guus Lachmeijer
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
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21
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Khan M, Cornelis SS, Khan MI, Elmelik D, Manders E, Bakker S, Derks R, Neveling K, van de Vorst M, Gilissen C, Meunier I, Defoort S, Puech B, Devos A, Schulz HL, Stöhr H, Grassmann F, Weber BHF, Dhaenens CM, Cremers FPM. Cost-effective molecular inversion probe-based ABCA4 sequencing reveals deep-intronic variants in Stargardt disease. Hum Mutat 2019; 40:1749-1759. [PMID: 31212395 DOI: 10.1002/humu.23787] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 02/11/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Stargardt disease (STGD1) is caused by biallelic mutations in ABCA4, but many patients are genetically unsolved due to insensitive mutation-scanning methods. We aimed to develop a cost-effective sequencing method for ABCA4 exons and regions carrying known causal deep-intronic variants. METHODS Fifty exons and 12 regions containing 14 deep-intronic variants of ABCA4 were sequenced using double-tiled single molecule Molecular Inversion Probe (smMIP)-based next-generation sequencing. DNAs of 16 STGD1 cases carrying 29 ABCA4 alleles and of four healthy persons were sequenced using 483 smMIPs. Thereafter, DNAs of 411 STGD1 cases with one or no ABCA4 variant were sequenced. The effect of novel noncoding variants on splicing was analyzed using in vitro splice assays. RESULTS Thirty-four ABCA4 variants previously identified in 16 STGD1 cases were reliably identified. In 155/411 probands (38%), two causal variants were identified. We identified 11 deep-intronic variants present in 62 alleles. Two known and two new noncanonical splice site variants showed splice defects, and one novel deep-intronic variant (c.4539+2065C>G) resulted in a 170-nt mRNA pseudoexon insertion (p.[Arg1514Lysfs*35,=]). CONCLUSIONS smMIPs-based sequence analysis of coding and selected noncoding regions of ABCA4 enabled cost-effective mutation detection in STGD1 cases in previously unsolved cases.
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Affiliation(s)
- 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
| | - Stéphanie S Cornelis
- 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
| | - Muhammad Imran 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
| | - Duaa Elmelik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eline Manders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sem Bakker
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Isabelle Meunier
- Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France
| | - Sabine Defoort
- Service d'exploration de la vision et neuro-ophtalmologie, CHRU de Lille, Lille, France
| | - Bernard Puech
- Service d'exploration de la vision et neuro-ophtalmologie, CHRU de Lille, Lille, France
| | - Aurore Devos
- University of Lille, INSERM UMR-S1172, CHU Lille, Biochemistry and Molecular Biology Department, UF Genopathies, Lille, France
| | - Heidi L Schulz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Claire-Marie Dhaenens
- University of Lille, INSERM UMR-S1172, CHU Lille, Biochemistry and Molecular Biology Department, UF Genopathies, Lille, France
| | - 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
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22
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Grolleman JE, de Voer RM, Elsayed FA, Nielsen M, Weren RDA, Palles C, Ligtenberg MJL, Vos JR, Ten Broeke SW, de Miranda NFCC, Kuiper RA, Kamping EJ, Jansen EAM, Vink-Börger ME, Popp I, Lang A, Spier I, Hüneburg R, James PA, Li N, Staninova M, Lindsay H, Cockburn D, Spasic-Boskovic O, Clendenning M, Sweet K, Capellá G, Sjursen W, Høberg-Vetti H, Jongmans MC, Neveling K, Geurts van Kessel A, Morreau H, Hes FJ, Sijmons RH, Schackert HK, Ruiz-Ponte C, Dymerska D, Lubinski J, Rivera B, Foulkes WD, Tomlinson IP, Valle L, Buchanan DD, Kenwrick S, Adlard J, Dimovski AJ, Campbell IG, Aretz S, Schindler D, van Wezel T, Hoogerbrugge N, Kuiper RP. Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype. Cancer Cell 2019; 35:256-266.e5. [PMID: 30753826 DOI: 10.1016/j.ccell.2018.12.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [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: 06/01/2018] [Revised: 09/17/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023]
Abstract
Biallelic germline mutations affecting NTHL1 predispose carriers to adenomatous polyposis and colorectal cancer, but the complete phenotype is unknown. We describe 29 individuals carrying biallelic germline NTHL1 mutations from 17 families, of which 26 developed one (n = 10) or multiple (n = 16) malignancies in 14 different tissues. An unexpected high breast cancer incidence was observed in female carriers (60%). Mutational signature analysis of 14 tumors from 7 organs revealed that NTHL1 deficiency underlies the main mutational process in all but one of the tumors (93%). These results reveal NTHL1 as a multi-tumor predisposition gene with a high lifetime risk for extracolonic cancers and a typical mutational signature observed across tumor types, which can assist in the recognition of this syndrome.
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Affiliation(s)
- Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Robbert D A Weren
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Janet R Vos
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Renske A Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M Elisa Vink-Börger
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Isabell Popp
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Alois Lang
- Vorarlberg Cancer Registry, Agency for Preventive and Social Medicine, Bregenz 6900, Austria
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany; Department of Internal Medicine I, University of Bonn, 53127 Bonn, Germany
| | - Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbournem, VIC 3000, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marija Staninova
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Helen Lindsay
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - David Cockburn
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | | | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Kevin Sweet
- Division of Human Genetics, Ohio State University Medical Centre, Columbus, OH 43221, USA
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs University Hospital, 7030 Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia 15706, Spain
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Ian P Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Sue Kenwrick
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service and University of Leeds, Leeds LS7 4SA, UK
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CT Utrecht, The Netherlands.
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23
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Holtgrewe M, Knaus A, Hildebrand G, Pantel JT, Santos MRDL, Neveling K, Goldmann J, Schubach M, Jäger M, Coutelier M, Mundlos S, Beule D, Sperling K, Krawitz PM. Multisite de novo mutations in human offspring after paternal exposure to ionizing radiation. Sci Rep 2018; 8:14611. [PMID: 30279461 PMCID: PMC6168503 DOI: 10.1038/s41598-018-33066-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 05/25/2018] [Accepted: 09/12/2018] [Indexed: 12/30/2022] Open
Abstract
A genome-wide evaluation of the effects of ionizing radiation on mutation induction in the mouse germline has identified multisite de novo mutations (MSDNs) as marker for previous exposure. Here we present the results of a small pilot study of whole genome sequencing in offspring of soldiers who served in radar units on weapon systems that were emitting high-frequency radiation. We found cases of exceptionally high MSDN rates as well as an increased mean in our cohort: While a MSDN mutation is detected in average in 1 out of 5 offspring of unexposed controls, we observed 12 MSDNs in altogether 18 offspring, including a family with 6 MSDNs in 3 offspring. Moreover, we found two translocations, also resulting from neighboring mutations. Our findings indicate that MSDNs might be suited in principle for the assessment of DNA damage from ionizing radiation also in humans. However, as exact person-related dose values in risk groups are usually not available, the interpretation of MSDNs in single families would benefit from larger molecular epidemiologic studies on this new biomarker.
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Affiliation(s)
- Manuel Holtgrewe
- Berlin Institute of Health (BIH), Core Unit Bioinformatics, Berlin, 10178, Germany.,Charité - Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, Rheinische Friedrich-Wilhelms Universität, Bonn, 53127, Germany
| | - Gabriele Hildebrand
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | - Jean-Tori Pantel
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | | | - Kornelia Neveling
- Department for Human Genetics, Radboud University, Nijmegen, 6525, Netherlands
| | - Jakob Goldmann
- Department for Human Genetics, Radboud University, Nijmegen, 6525, Netherlands
| | - Max Schubach
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany.,Berlin Institute of Health (BIH), JRG Computational Genome Biology, 10178, Berlin, Germany
| | - Marten Jäger
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | - Marie Coutelier
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | - Stefan Mundlos
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health (BIH), Core Unit Bioinformatics, Berlin, 10178, Germany.,Max Delbrück Center for Molecuar Medicine, 13125, Berlin, Germany
| | - Karl Sperling
- Charité - Universitätsmedizin Berlin, Institute of Medical and Human Genetics, 13353, Berlin, Germany
| | - Peter Michael Krawitz
- Institute for Genomic Statistics and Bioinformatics, Rheinische Friedrich-Wilhelms Universität, Bonn, 53127, Germany.
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24
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Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SMM, Adan IBJF, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJL, Shendure J, Nelen MR, Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem 2016; 63:503-512. [PMID: 27974384 DOI: 10.1373/clinchem.2016.263897] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Bart van Lier
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Alwin Rikken
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Tychon
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stijn M M Bertens
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Ivo B J F Adan
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bastiaan B Tops
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tomasz Stokowy
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hildegunn Høberg-Vetti
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Evan Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marcel R Nelen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands;
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
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25
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Eijkelenboom A, Kamping EJ, Kastner-van Raaij AW, Hendriks-Cornelissen SJ, Neveling K, Kuiper RP, Hoischen A, Nelen MR, Ligtenberg MJ, Tops BB. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. J Mol Diagn 2016; 18:851-863. [DOI: 10.1016/j.jmoldx.2016.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
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26
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Spiegler S, Kirchmaier B, Rath M, Korenke GC, Tetzlaff F, van de Vorst M, Neveling K, Acker-Palmer A, Kuss AW, Gilissen C, Fischer A, Schulte-Merker S, Felbor U. FAM222B Is Not a Likely Novel Candidate Gene for Cerebral Cavernous Malformations. Mol Syndromol 2016; 7:144-52. [PMID: 27587990 DOI: 10.1159/000446884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2016] [Indexed: 12/11/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are prevalent slow-flow vascular lesions which harbour the risk to develop intracranial haemorrhages, focal neurological deficits, and epileptic seizures. Autosomal dominantly inherited CCMs were found to be associated with heterozygous inactivating mutations in 3 genes, CCM1 (KRIT1), CCM2 (MGC4607), and CCM3 (PDCD10) in 1999, 2003 and 2005, respectively. Despite the availability of high-throughput sequencing techniques, no further CCM gene has been published since. Here, we report on the identification of an autosomal dominantly inherited frameshift mutation in a gene of thus far unknown function, FAM222B (C17orf63), through exome sequencing of CCM patients mutation-negative for CCM1-3. A yeast 2-hybrid screen revealed interactions of FAM222B with the tubulin cytoskeleton and STAMBP which is known to be associated with microcephaly-capillary malformation syndrome. However, a phenotype similar to existing models was not found, neither in fam222bb/fam222ba double mutant zebrafish generated by transcription activator-like effector nucleases nor in an in vitro sprouting assay using human umbilical vein endothelial cells transfected with siRNA against FAM222B. These observations led to the assumption that aberrant FAM222B is not involved in the formation of CCMs.
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Affiliation(s)
- Stefanie Spiegler
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Bettina Kirchmaier
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences (BMLS), University of Frankfurt, Frankfurt am Main, Germany; Hubrecht Institute - KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Matthias Rath
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | | | - Fabian Tetzlaff
- Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Amparo Acker-Palmer
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences (BMLS), University of Frankfurt, Frankfurt am Main, Germany
| | - Andreas W Kuss
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Andreas Fischer
- Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Cells-in-Motion Cluster of Excellence, Faculty of Medicine, University of Münster, Münster, Germany; Hubrecht Institute - KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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Duvvari MR, van de Ven JPH, Geerlings MJ, Saksens NTM, Bakker B, Henkes A, Neveling K, del Rosario M, Westra D, van den Heuvel LPWJ, Schick T, Fauser S, Boon CJF, Hoyng CB, de Jong EK, den Hollander AI. Whole Exome Sequencing in Patients with the Cuticular Drusen Subtype of Age-Related Macular Degeneration. PLoS One 2016; 11:e0152047. [PMID: 27007659 PMCID: PMC4805164 DOI: 10.1371/journal.pone.0152047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 03/08/2016] [Indexed: 12/20/2022] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in elderly people worldwide. Cuticular drusen (CD) is a clinical subtype of AMD, which typically displays an earlier age at onset, and has a strong genetic component. Genetic studies support a role for rare sequence variants in CD susceptibility, and rare sequence variants in the CFH gene have been identified in 8.8% of CD cases. To further explore the role of rare variants in CD, we performed whole exome sequencing (WES) in 14 affected members of six families and 12 sporadic cases with CD. We detected rare sequence variants in CFH and FBLN5, which previously were shown to harbor rare variants in patients with CD. In addition, we detected heterozygous rare sequence variants in several genes encoding components of the extracellular matrix (ECM), including FBLN1, FBLN3/EFEMP1, FBLN5, FBLN6/HMCN1, FBN2, and COL15A1. Two rare pathogenic variants were identified in the COL15A1 gene: one in a sporadic case and another was found to segregate in a family with six affected individuals with CD. In addition, two rare pathogenic variants were identified in the FGL1 gene in three unrelated CD cases. These findings suggest that alterations in the ECM and in the coagulation pathway may play a role in the pathogenesis of CD. The identified candidate genes require further analyses in larger cohorts to confirm their role in the CD subtype of AMD. No evidence was found of rare sequence variants in a single gene that segregate with CD in the six families, suggesting that the disease is genetically heterogeneous.
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Affiliation(s)
- Maheswara R. Duvvari
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Maartje J. Geerlings
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Nicole T. M. Saksens
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Bjorn Bakker
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Arjen Henkes
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marisol del Rosario
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Dineke Westra
- Department of Pediatric Nephrology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Camiel J. F. Boon
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Eiko K. de Jong
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Anneke I. den Hollander
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
- * E-mail:
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28
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Neveling K, Tjwan Thung D, Beulen L, van Rens-Buijsman W, Gomes I, van den Heuvel S, Mieloo H, Derks-Prinsen I, Kater-Baats E, Faas BHW. Validation of two-channel sequencing-by-synthesis for noninvasive prenatal testing of fetal whole and partial chromosome aberrations. Prenat Diagn 2016; 36:216-23. [PMID: 26774010 DOI: 10.1002/pd.4777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To validate Illumina's two-channel NextSeq 500 sequencing system for noninvasive prenatal testing (NIPT) of fetal whole chromosome and partial aberrations. METHODS A total of 162 plasma samples, previously sequenced for NIPT on a SOLiD 5500xl platform, were sequenced on the NextSeq 500 using 75-bp single-end sequencing, followed by analysis using the WISECONDOR algorithm. RESULTS For whole chromosome aneuploidy detection, all samples were classified correctly (in total 3× T13, 3× T18, 8× T21 and 145× euploid). Three partial aberrations (36-Mb terminal loss of 5p, 14-Mb gain on 18p and 33-Mb terminal loss of 13q) were also correctly identified. Fetal fractions in 34 male samples sequenced on both the SOLiD 5500xl and NextSeq 500 platform showed no significant difference. To test robustness, two sample sets, containing both euploid and aneuploid samples, were sequenced on different NextSeq 500 machines, revealing identical results. With unchanged laboratory flow, the NIPT turnaround time could be reduced from 15-16 calendar days to 7-8 calendar days, after switching from the SOLiD 5500xl to the NextSeq 500 platform. CONCLUSIONS The NextSeq 500 platform can be used for NIPT to detect both whole and partial chromosome aberrations. It has fast turnaround times and is suitable for mid-sized laboratories.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands.,Prenatal Screening Foundation Nijmegen Region, Nijmegen, The Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lean Beulen
- Prenatal Screening Foundation Nijmegen Region, Nijmegen, The Netherlands.,Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wendy van Rens-Buijsman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingrid Gomes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hanneke Mieloo
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Irma Derks-Prinsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigitte H W Faas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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29
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Weren RDA, Venkatachalam R, Cazier JB, Farin HF, Kets CM, de Voer RM, Vreede L, Verwiel ETP, van Asseldonk M, Kamping EJ, Kiemeney LA, Neveling K, Aben KKH, Carvajal-Carmona L, Nagtegaal ID, Schackert HK, Clevers H, van de Wetering M, Tomlinson IP, Ligtenberg MJL, Hoogerbrugge N, Geurts van Kessel A, Kuiper RP. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. J Pathol 2015; 236:155-64. [PMID: 25712196 PMCID: PMC6681464 DOI: 10.1002/path.4520] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/09/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
Abstract
Heritable genetic variants can significantly affect the lifetime risk of developing cancer, including polyposis and colorectal cancer (CRC). Variants in genes currently known to be associated with a high risk for polyposis or CRC, however, explain only a limited number of hereditary cases. The identification of additional genetic causes is, therefore, crucial to improve CRC prevention, detection and treatment. We have performed genome-wide and targeted DNA copy number profiling and resequencing in early-onset and familial polyposis/CRC patients, and show that deletions affecting the open reading frame of the tumour suppressor gene FOCAD are recurrent and significantly enriched in CRC patients compared with unaffected controls. All patients carrying FOCAD deletions exhibited a personal or family history of polyposis. RNA in situ hybridization revealed FOCAD expression in epithelial cells in the colonic crypt, the site of tumour initiation, as well as in colonic tumours and organoids. Our data suggest that monoallelic germline deletions in the tumour suppressor gene FOCAD underlie moderate genetic predisposition to the development of polyposis and CRC.
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Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Henner F Farin
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | - C Marleen Kets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lilian Vreede
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Eugène T P Verwiel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Monique van Asseldonk
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Luis Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, CA, USA
| | - Iris D Nagtegaal
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Hans Clevers
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | | | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics University of Oxford, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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30
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Diekstra A, Bosgoed E, Rikken A, van Lier B, Kamsteeg EJ, Tychon M, Derks RC, van Soest RA, Mensenkamp AR, Scheffer H, Neveling K, Nelen MR. Translating sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing. Clin Chem 2014; 61:154-62. [PMID: 25274553 DOI: 10.1373/clinchem.2014.225250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic laboratories, enabling the sequencing of large targeted gene panels or exomes. The development of benchtop NGS instruments now allows the analysis of single genes or small gene panels, making these platforms increasingly competitive with Sanger sequencing. METHODS We developed a generic automated ion semiconductor sequencing work flow that can be used in a clinical setting and can serve as a substitute for Sanger sequencing. Standard amplicon-based enrichment remained identical to PCR for Sanger sequencing. A novel postenrichment pooling strategy was developed, limiting the number of library preparations and reducing sequencing costs up to 70% compared to Sanger sequencing. RESULTS A total of 1224 known pathogenic variants were analyzed, yielding an analytical sensitivity of 99.92% and specificity of 99.99%. In a second experiment, a total of 100 patient-derived DNA samples were analyzed using a blind analysis. The results showed an analytical sensitivity of 99.60% and specificity of 99.98%, comparable to Sanger sequencing. CONCLUSIONS Ion semiconductor sequencing can be a first choice mutation scanning technique, independent of the genes analyzed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hans Scheffer
- Department of Human Genetics and Donders Center for Neurosciences, Radboud university medical center, Nijmegen, the Netherlands
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31
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de Koning HD, van Gijn ME, Stoffels M, Jongekrijg J, Zeeuwen PLJM, Elferink MG, Nijman IJ, Jansen PAM, Neveling K, van der Meer JWM, Schalkwijk J, Simon A. Myeloid lineage-restricted somatic mosaicism of NLRP3 mutations in patients with variant Schnitzler syndrome. J Allergy Clin Immunol 2014; 135:561-4. [PMID: 25239704 DOI: 10.1016/j.jaci.2014.07.050] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/29/2014] [Accepted: 07/23/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Heleen D de Koning
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands.
| | - Mariëlle E van Gijn
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Monique Stoffels
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
| | - Johanna Jongekrijg
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
| | - Martin G Elferink
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Patrick A M Jansen
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease (IGMD), Nijmegen, The Netherlands
| | - Jos W M van der Meer
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands.
| | - Anna Simon
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands; Nijmegen Center for Immunodeficiency and Autoinflammation, Nijmegen, The Netherlands
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32
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Seco CZ, Oonk AMM, Domínguez-Ruiz M, Draaisma JMT, Gandía M, Oostrik J, Neveling K, Kunst HPM, Hoefsloot LH, del Castillo I, Pennings RJE, Kremer H, Admiraal RJC, Schraders M. Progressive hearing loss and vestibular dysfunction caused by a homozygous nonsense mutation in CLIC5. Eur J Hum Genet 2014; 23:189-94. [PMID: 24781754 DOI: 10.1038/ejhg.2014.83] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 03/20/2014] [Accepted: 04/04/2014] [Indexed: 11/10/2022] Open
Abstract
In a consanguineous Turkish family diagnosed with autosomal recessive nonsyndromic hearing impairment (arNSHI), a homozygous region of 47.4 Mb was shared by the two affected siblings on chromosome 6p21.1-q15. This region contains 247 genes including the known deafness gene MYO6. No pathogenic variants were found in MYO6, neither with sequence analysis of the coding region and splice sites nor with mRNA analysis. Subsequent candidate gene evaluation revealed CLIC5 as an excellent candidate gene. The orthologous mouse gene is mutated in the jitterbug mutant that exhibits progressive hearing impairment and vestibular dysfunction. Mutation analysis of CLIC5 revealed a homozygous nonsense mutation c.96T>A (p.(Cys32Ter)) that segregated with the hearing loss. Further analysis of CLIC5 in 213 arNSHI patients from mostly Dutch and Spanish origin did not reveal any additional pathogenic variants. CLIC5 mutations are thus not a common cause of arNSHI in these populations. The hearing loss in the present family had an onset in early childhood and progressed from mild to severe or even profound before the second decade. Impaired hearing is accompanied by vestibular areflexia and in one of the patients with mild renal dysfunction. Although we demonstrate that CLIC5 is expressed in many other human tissues, no additional symptoms were observed in these patients. In conclusion, our results show that CLIC5 is a novel arNSHI gene involved in progressive hearing impairment, vestibular and possibly mild renal dysfunction in a family of Turkish origin.
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Affiliation(s)
- Celia Zazo Seco
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne M M Oonk
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - María Domínguez-Ruiz
- 1] Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain [2] Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jos M T Draaisma
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marta Gandía
- 1] Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain [2] Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jaap Oostrik
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- 1] Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands [2] Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Henricus P M Kunst
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lies H Hoefsloot
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
| | - Ronald J E Pennings
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands [4] Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margit Schraders
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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33
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Ajmal M, Khan MI, Neveling K, Khan YM, Azam M, Waheed NK, Hamel CP, Ben-Yosef T, De Baere E, Koenekoop RK, Collin RWJ, Qamar R, Cremers FPM. A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma. J Med Genet 2014; 51:444-8. [PMID: 24737827 DOI: 10.1136/jmedgenet-2014-102316] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is the most frequent inherited retinal disease, which shows a relatively high incidence of the autosomal-recessive form in Pakistan. METHODS Genome-wide high-density single-nucleotide polymorphism (SNP) microarrays were used to identify homozygous regions shared by affected individuals of one consanguineous family. DNA of three affected and two healthy siblings was used for SNP genotyping. Genotyping data were then analysed by Homozygosity Mapper. DNA of the proband was further analysed employing exome sequencing. RESULTS Homozygosity mapping revealed a single homozygous region on chromosome 16, shared by three affected individuals. Subsequent exome sequencing identified a novel missense mutation, c.995G>A; p.(Gly332Asp), in DHX38. This mutation was found to be present in a homozygous state in four affected individuals while two healthy siblings and the parents of the affected persons were heterozygous for this mutation. This variant thereby yields a logarithm of the odds (LOD) score of 3.25, which is highly suggestive for linkage. This variant was neither detected in 180 ethnically matched control individuals, nor in 7540 Africans or Caucasians and an in-house database that contained the exome data of 400 individuals. CONCLUSIONS By combining genome-wide homozygosity mapping and exome sequencing, a novel missense mutation was identified in the DHX38 gene that encodes the pre-mRNA splicing factor PRP16, in a Pakistani family with early-onset autosomal-recessive RP. The phenotype is different from those associated with other retinal pre-mRNA splicing factors and DHX38 is the first pre-mRNA splicing gene that is putatively associated with autosomal-recessive inherited RP.
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Affiliation(s)
- Muhammad Ajmal
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad Imran Khan
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yar Muhammad Khan
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Department of Chemistry, University of Science and Technology, Bannu, Pakistan
| | - Maleeha Azam
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Christian P Hamel
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U, Université Paris Descartes-Sorbonne Paris Cité, Montpellier, France
| | - Tamar Ben-Yosef
- Department of Genetics, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Robert K Koenekoop
- Department of Paediatric Surgery, Human Genetics and Ophthalmology, McGill University Health Centre, Montreal, Canada
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Raheel Qamar
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
| | - Frans P M Cremers
- Faculty of Science, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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Siemiatkowska AM, Stoffels M, Neveling K, Simon A, van Hagen PM, den Hollander AI, Cremers FP, van den Born LI, Collin RW. OR11-002 - Mutations in MVK cause non-syndromic RP. Pediatr Rheumatol Online J 2013. [PMCID: PMC3952182 DOI: 10.1186/1546-0096-11-s1-a191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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De Koning HD, Schalkwijk J, van der Meer JW, Zeeuwen PL, Neveling K, van Gijn M, Simon A. PW03-007 - NLRP3 genetic variants in Schnitzler’s syndrome. Pediatr Rheumatol Online J 2013. [PMCID: PMC3952268 DOI: 10.1186/1546-0096-11-s1-a233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Neveling K, Feenstra I, Gilissen C, Hoefsloot LH, Kamsteeg EJ, Mensenkamp AR, Rodenburg RJT, Yntema HG, Spruijt L, Vermeer S, Rinne T, van Gassen KL, Bodmer D, Lugtenberg D, de Reuver R, Buijsman W, Derks RC, Wieskamp N, van den Heuvel B, Ligtenberg MJL, Kremer H, Koolen DA, van de Warrenburg BPC, Cremers FPM, Marcelis CLM, Smeitink JAM, Wortmann SB, van Zelst-Stams WAG, Veltman JA, Brunner HG, Scheffer H, Nelen MR. A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum Mutat 2013; 34:1721-6. [PMID: 24123792 DOI: 10.1002/humu.22450] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [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: 04/12/2013] [Accepted: 09/04/2013] [Indexed: 01/20/2023]
Abstract
The advent of massive parallel sequencing is rapidly changing the strategies employed for the genetic diagnosis and research of rare diseases that involve a large number of genes. So far it is not clear whether these approaches perform significantly better than conventional single gene testing as requested by clinicians. The current yield of this traditional diagnostic approach depends on a complex of factors that include gene-specific phenotype traits, and the relative frequency of the involvement of specific genes. To gauge the impact of the paradigm shift that is occurring in molecular diagnostics, we assessed traditional Sanger-based sequencing (in 2011) and exome sequencing followed by targeted bioinformatics analysis (in 2012) for five different conditions that are highly heterogeneous, and for which our center provides molecular diagnosis. We find that exome sequencing has a much higher diagnostic yield than Sanger sequencing for deafness, blindness, mitochondrial disease, and movement disorders. For microsatellite-stable colorectal cancer, this was low under both strategies. Even if all genes that could have been ordered by physicians had been tested, the larger number of genes captured by the exome would still have led to a clearly superior diagnostic yield at a fraction of the cost.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease, Radboud university medical centre, Nijmegen, The Netherlands
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Schuurs-Hoeijmakers JHM, Vulto-van Silfhout AT, Vissers LELM, van de Vondervoort IIGM, van Bon BWM, de Ligt J, Gilissen C, Hehir-Kwa JY, Neveling K, del Rosario M, Hira G, Reitano S, Vitello A, Failla P, Greco D, Fichera M, Galesi O, Kleefstra T, Greally MT, Ockeloen CW, Willemsen MH, Bongers EMHF, Janssen IM, Pfundt R, Veltman JA, Romano C, Willemsen MA, van Bokhoven H, Brunner HG, de Vries BBA, de Brouwer APM. Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing. J Med Genet 2013; 50:802-11. [PMID: 24123876 DOI: 10.1136/jmedgenet-2013-101644] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Intellectual disability (ID) is a common neurodevelopmental disorder affecting 1-3% of the general population. Mutations in more than 10% of all human genes are considered to be involved in this disorder, although the majority of these genes are still unknown. OBJECTIVES We investigated 19 small non-consanguineous families with two to five affected siblings in order to identify pathogenic gene variants in known, novel and potential ID candidate genes. Non-consanguineous families have been largely ignored in gene identification studies as small family size precludes prior mapping of the genetic defect. METHODS AND RESULTS Using exome sequencing, we identified pathogenic mutations in three genes, DDHD2, SLC6A8, and SLC9A6, of which the latter two have previously been implicated in X-linked ID phenotypes. In addition, we identified potentially pathogenic mutations in BCORL1 on the X-chromosome and in MCM3AP, PTPRT, SYNE1, and ZNF528 on autosomes. CONCLUSIONS We show that potentially pathogenic gene variants can be identified in small, non-consanguineous families with as few as two affected siblings, thus emphasising their value in the identification of syndromic and non-syndromic ID genes.
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Siemiatkowska AM, van den Born LI, van Hagen PM, Stoffels M, Neveling K, Henkes A, Kipping-Geertsema M, Hoefsloot LH, Hoyng CB, Simon A, den Hollander AI, Cremers FPM, Collin RWJ. Mutations in the mevalonate kinase (MVK) gene cause nonsyndromic retinitis pigmentosa. Ophthalmology 2013; 120:2697-2705. [PMID: 24084495 DOI: 10.1016/j.ophtha.2013.07.052] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVE Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous disorder characterized by night blindness and peripheral vision loss, and in many cases leads to blindness. Despite extensive knowledge about genes involved in the pathogenesis of RP, the genetic cause remains elusive in many patients. In this study, we aimed to identify novel genes that are involved in the cause of RP. DESIGN We present a case series with mutations in the mevalonate kinase (MVK) gene. PARTICIPANTS A total of 769 patients with nonsyndromic RP and 174 Dutch control individuals participated in this study. METHODS Exome sequencing analysis was performed in a proband of Dutch origin who was initially diagnosed with nonsyndromic autosomal recessive RP. Mutations in MVK were identified and subsequently tested for segregation within the patient's family and screened in a large cohort of patients with genetically unsolved RP. Patients with mutations underwent extensive clinical reexamination. MAIN OUTCOME MEASURES Digital fundus photography, spectral-domain optical coherence tomography (OCT), and fundus autofluorescence analysis were performed in patients with MVK mutations. Mevalonate kinase (MK) enzyme activity was analyzed in cultured lymphoblastoid cells, and mevalonic acid levels were measured in urine samples. RESULTS Exome variant filtering and prioritization led to the identification of compound heterozygous mutations in MVK (p.I268T and p.A334T) in the proband and her affected brother. Screening of our nonsyndromic RP patient cohort revealed an additional individual who was homozygous for the p.A334T alteration. Clinical reevaluation of all 3 patients showed a classic form of RP with variable extraocular symptoms, such as history of recurrent childhood febrile crises in 2 patients, mild ataxia in 1, and renal failure in 1. All 3 affected individuals showed a significantly decreased MK activity and highly elevated levels of urinary mevalonic acid. CONCLUSIONS Although the MK activity in cells and mevalonic acid concentrations in urine are strongly aberrant and comparable to that in patients with systemic mevalonate kinase deficiency (MKD), only mild clinical symptoms related to this syndrome were observed in our patients. In the current article, we add another phenotype to the spectrum of diverging disorders associated with mutations in MVK.
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Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - P Martin van Hagen
- Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Monique Stoffels
- Department of General Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Infection, Inflammation and Immunity (N4i), Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Arjen Henkes
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - Lies H Hoefsloot
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anna Simon
- Department of General Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Infection, Inflammation and Immunity (N4i), Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands.
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Keupp K, Li Y, Vargel I, Hoischen A, Richardson R, Neveling K, Alanay Y, Uz E, Elcioğlu N, Rachwalski M, Kamaci S, Tunçbilek G, Akin B, Grötzinger J, Konas E, Mavili E, Müller-Newen G, Collmann H, Roscioli T, Buckley MF, Yigit G, Gilissen C, Kress W, Veltman J, Hammerschmidt M, Akarsu NA, Wollnik B. Mutations in the interleukin receptor IL11RA cause autosomal recessive Crouzon-like craniosynostosis. Mol Genet Genomic Med 2013; 1:223-37. [PMID: 24498618 PMCID: PMC3865590 DOI: 10.1002/mgg3.28] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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: 04/24/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 12/20/2022] Open
Abstract
We have characterized a novel autosomal recessive Crouzon-like craniosynostosis syndrome in a 12-affected member family from Antakya, Turkey, the presenting features of which include: multiple suture synostosis, midface hypoplasia, variable degree of exophthalmos, relative prognathism, a beaked nose, and conductive hearing loss. Homozygosity mapping followed by targeted next-generation sequencing identified a c.479+6T>G mutation in the interleukin 11 receptor alpha gene (IL11RA) on chromosome 9p21. This donor splice-site mutation leads to a high percentage of aberrant IL11RA mRNA transcripts in an affected individual and altered mRNA splicing determined by in vitro exon trapping. An extended IL11RA mutation screen was performed in a cohort of 79 patients with an initial clinical diagnosis of Crouzon syndrome, pansynostosis, or unclassified syndromic craniosynostosis. We identified mutations segregating with the disease in five families: a German patient of Turkish origin and a Turkish family with three affected sibs all of whom were homozygous for the previously identified IL11RA c.479+6T>G mutation; a family with pansynostosis with compound heterozygous missense mutations, p.Pro200Thr and p.Arg237Pro; and two further Turkish families with Crouzon-like syndrome carrying the homozygous nonsense mutations p.Tyr232* and p.Arg292*. Using transient coexpression in HEK293T and COS7 cells, we demonstrated dramatically reduced IL11-mediated STAT3 phosphorylation for all mutations. Immunofluorescence analysis of mouse Il11ra demonstrated specific protein expression in cranial mesenchyme which was localized around the coronal suture tips and in the lambdoidal suture. In situ hybridization analysis of adult zebrafish also detected zfil11ra expression in the coronal suture between the overlapping frontal and parietal plates. This study demonstrates that mutations in the IL11RA gene cause an autosomal recessive Crouzon-like craniosynostosis.
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Affiliation(s)
- Katharina Keupp
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Institute of Human Genetics, University of Cologne 50931, Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne 50931, Cologne, Germany
| | - Yun Li
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Institute of Human Genetics, University of Cologne 50931, Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne 50931, Cologne, Germany
| | - Ibrahim Vargel
- Department of Plastic and Reconstructive Surgery, Hacettepe University Medical Faculty 06100, Ankara, Turkey ; Department of Plastic and Reconstructive Surgery, Medical Faculty, Kirikkale University 71100, Kirikkale, Turkey
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands
| | - Rebecca Richardson
- Department of Physiology and Pharmacology, University of Bristol BS8 1TD Bristol, U.K
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands
| | - Yasemin Alanay
- Department of Pediatrics, Pediatric Genetics Unit, Hacettepe University Medical Faculty 06100, Ankara, Turkey ; Department of Pediatrics, Pediatric Genetics Unit, Acibadem University 34457, İstanbul, Turkey
| | - Elif Uz
- Department of Medical Genetics, Gene Mapping Laboratory, Hacettepe University Medical Faculty 06100, Ankara, Turkey ; Department of Biology, Duzce University 81620, Duzce, Turkey
| | - Nursel Elcioğlu
- Department of Pediatric Genetics, Marmara University Medical Faculty 34668, Istanbul, Turkey
| | - Martin Rachwalski
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Institute of Human Genetics, University of Cologne 50931, Cologne, Germany
| | - Soner Kamaci
- Department of Orthodontics, Hacettepe University Faculty of Dentistry 06100, Ankara, Turkey
| | - Gökhan Tunçbilek
- Department of Plastic and Reconstructive Surgery, Hacettepe University Medical Faculty 06100, Ankara, Turkey
| | - Burcu Akin
- Department of Medical Genetics, Gene Mapping Laboratory, Hacettepe University Medical Faculty 06100, Ankara, Turkey
| | - Joachim Grötzinger
- Medical Faculty, Institute of Biochemistry, University of Kiel 24118, Kiel, Germany
| | - Ersoy Konas
- Department of Plastic and Reconstructive Surgery, Hacettepe University Medical Faculty 06100, Ankara, Turkey
| | - Emin Mavili
- Department of Plastic and Reconstructive Surgery, Hacettepe University Medical Faculty 06100, Ankara, Turkey
| | - Gerhard Müller-Newen
- Medical Faculty, Institute of Biochemistry and Molecular Biology, RWTH Aachen University 52074, Aachen, Germany
| | - Hartmut Collmann
- Department for Neurosurgery, Medical Faculty, University of Würzburg 97070, Würzburg, Germany
| | - Tony Roscioli
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands ; Department of Haematology and Genetics, South Eastern Area Laboratory Services 2031, Sydney, Australia
| | - Michael F Buckley
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands ; Department of Haematology and Genetics, South Eastern Area Laboratory Services 2031, Sydney, Australia
| | - Gökhan Yigit
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Institute of Human Genetics, University of Cologne 50931, Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne 50931, Cologne, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands
| | - Wolfram Kress
- Medical Faculty, Institute of Human Genetics, University of Würzburg 97047, Würzburg, Germany
| | - Joris Veltman
- Department of Human Genetics, Radboud University Nijmegen Medical Centre 6500HB, Nijmegen, The Netherlands
| | - Matthias Hammerschmidt
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne 50931, Cologne, Germany ; Institute of Developmental Biology, University of Cologne 50674, Cologne, Germany
| | - Nurten A Akarsu
- Department of Medical Genetics, Gene Mapping Laboratory, Hacettepe University Medical Faculty 06100, Ankara, Turkey
| | - Bernd Wollnik
- Center for Molecular Medicine Cologne (CMMC), University of Cologne 50931, Cologne, Germany ; Institute of Human Genetics, University of Cologne 50931, Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne 50931, Cologne, Germany
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Neveling K, Collin RW, Gilissen C, van Huet RA, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FP, Scheffer H. Next Generation Genetic Testing for Retinitis Pigmentosa. Hum Mutat 2013. [DOI: 10.1002/humu.22357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Voigt C, Mégarbané A, Neveling K, Czeschik JC, Albrecht B, Callewaert B, von Deimling F, Hehr A, Falkenberg Smeland M, König R, Kuechler A, Marcelis C, Puiu M, Reardon W, Riise Stensland HMF, Schweiger B, Steehouwer M, Teller C, Martin M, Rahmann S, Hehr U, Brunner HG, Lüdecke HJ, Wieczorek D. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations. Orphanet J Rare Dis 2013; 8:110. [PMID: 23879989 PMCID: PMC3727992 DOI: 10.1186/1750-1172-8-110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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: 04/10/2013] [Accepted: 07/05/2013] [Indexed: 12/25/2022] Open
Abstract
Background Mutations in EFTUD2 were proven to cause a very distinct mandibulofacial dysostosis type Guion-Almeida (MFDGA, OMIM #610536). Recently, gross deletions and mutations in EFTUD2 were determined to cause syndromic esophageal atresia (EA), as well. We set forth to find further conditions caused by mutations in the EFTUD2 gene (OMIM *603892). Methods and results We performed exome sequencing in two familial cases with clinical features overlapping with MFDGA and EA, but which were previously assumed to represent distinct entities, a syndrome with esophageal atresia, hypoplasia of zygomatic complex, microcephaly, cup-shaped ears, congenital heart defect, and intellectual disability in a mother and her two children [AJMG 143A(11):1135-1142, 2007] and a supposedly autosomal recessive oto-facial syndrome with midline malformations in two sisters [AJMG 132(4):398-401, 2005]. While the analysis of our exome data was in progress, a recent publication made EFTUD2 mutations highly likely in these families. This hypothesis could be confirmed with exome as well as with Sanger sequencing. Also, in three further sporadic patients, clinically overlapping to these two families, de novo mutations within EFTUD2 were identified by Sanger sequencing. Our clinical and molecular workup of the patients discloses a broad phenotypic spectrum, and describes for the first time an instance of germline mosaicism for an EFTUD2 mutation. Conclusions The clinical features of the eight patients described here further broaden the phenotypic spectrum caused by EFTUD2 mutations or deletions. We here show, that it not only includes mandibulofacial dysostosis type Guion-Almeida, which should be reclassified as an acrofacial dysostosis because of thumb anomalies (present in 12/35 or 34% of patients) and syndromic esophageal atresia [JMG 49(12). 737-746, 2012], but also the two new syndromes, namely oto-facial syndrome with midline malformations published by Mégarbané et al. [AJMG 132(4): 398-401, 2005] and the syndrome published by Wieczorek et al. [AJMG 143A(11): 1135-1142, 2007] The finding of mild phenotypic features in the mother of one family that could have been overlooked and the possibility of germline mosaicism in apparently healthy parents in the other family should be taken into account when counseling such families.
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Affiliation(s)
- Claudia Voigt
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
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Roosing S, Rohrschneider K, Beryozkin A, Sharon D, Weisschuh N, Staller J, Kohl S, Zelinger L, Peters T, Neveling K, Strom T, van den Born L, Hoyng C, Klaver C, Roepman R, Wissinger B, Banin E, Cremers F, den Hollander A, den Hollander AI. Mutations in RAB28, encoding a farnesylated small GTPase, are associated with autosomal-recessive cone-rod dystrophy. Am J Hum Genet 2013; 93:110-7. [PMID: 23746546 DOI: 10.1016/j.ajhg.2013.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 03/27/2013] [Accepted: 05/03/2013] [Indexed: 01/28/2023] Open
Abstract
The majority of the genetic causes of autosomal-recessive (ar) cone-rod dystrophy (CRD) are currently unknown. A combined approach of homozygosity mapping and exome sequencing revealed a homozygous nonsense mutation (c.565C>T [p.Glu189*]) in RAB28 in a German family with three siblings with arCRD. Another homozygous nonsense mutation (c.409C>T [p.Arg137*]) was identified in a family of Moroccan Jewish descent with two siblings affected by arCRD. All five affected individuals presented with hyperpigmentation in the macula, progressive loss of the visual acuity, atrophy of the retinal pigment epithelium, and severely reduced cone and rod responses on the electroretinogram. RAB28 encodes a member of the Rab subfamily of the RAS-related small GTPases. Alternative RNA splicing yields three predicted protein isoforms with alternative C-termini, which are all truncated by the nonsense mutations identified in the arCRD families in this report. Opposed to other Rab GTPases that are generally geranylgeranylated, RAB28 is predicted to be farnesylated. Staining of rat retina showed localization of RAB28 to the basal body and the ciliary rootlet of the photoreceptors. Analogous to the function of other RAB family members, RAB28 might be involved in ciliary transport in photoreceptor cells. This study reveals a crucial role for RAB28 in photoreceptor function and suggests that mutations in other Rab proteins may also be associated with retinal dystrophies.
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Neveling K, Martinez-Carrera L, Hölker I, Heister A, Verrips A, Hosseini-Barkooie S, Gilissen C, Vermeer S, Pennings M, Meijer R, te Riele M, Frijns C, Suchowersky O, MacLaren L, Rudnik-Schöneborn S, Sinke R, Zerres K, Lowry R, Lemmink H, Garbes L, Veltman J, Schelhaas H, Scheffer H, Wirth B. Mutations in BICD2, which encodes a golgin and important motor adaptor, cause congenital autosomal-dominant spinal muscular atrophy. Am J Hum Genet 2013; 92:946-54. [PMID: 23664116 DOI: 10.1016/j.ajhg.2013.04.011] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/15/2013] [Accepted: 04/15/2013] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a heterogeneous group of neuromuscular disorders caused by degeneration of lower motor neurons. Although functional loss of SMN1 is associated with autosomal-recessive childhood SMA, the genetic cause for most families affected by dominantly inherited SMA is unknown. Here, we identified pathogenic variants in bicaudal D homolog 2 (Drosophila) (BICD2) in three families afflicted with autosomal-dominant SMA. Affected individuals displayed congenital slowly progressive muscle weakness mainly of the lower limbs and congenital contractures. In a large Dutch family, linkage analysis identified a 9q22.3 locus in which exome sequencing uncovered c.320C>T (p.Ser107Leu) in BICD2. Sequencing of 23 additional families affected by dominant SMA led to the identification of pathogenic variants in one family from Canada (c.2108C>T [p.Thr703Met]) and one from the Netherlands (c.563A>C [p.Asn188Thr]). BICD2 is a golgin and motor-adaptor protein involved in Golgi dynamics and vesicular and mRNA transport. Transient transfection of HeLa cells with all three mutant BICD2 cDNAs caused massive Golgi fragmentation. This observation was even more prominent in primary fibroblasts from an individual harboring c.2108C>T (p.Thr703Met) (affecting the C-terminal coiled-coil domain) and slightly less evident in individuals with c.563A>C (p.Asn188Thr) (affecting the N-terminal coiled-coil domain). Furthermore, BICD2 levels were reduced in affected individuals and trapped within the fragmented Golgi. Previous studies have shown that Drosophila mutant BicD causes reduced larvae locomotion by impaired clathrin-mediated synaptic endocytosis in neuromuscular junctions. These data emphasize the relevance of BICD2 in synaptic-vesicle recycling and support the conclusion that BICD2 mutations cause congenital slowly progressive dominant SMA.
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Ajmal M, Khan MI, Neveling K, Tayyab A, Jaffar S, Sadeque A, Ayub H, Abbasi NM, Riaz M, Micheal S, Gilissen C, Ali SHB, Azam M, Collin RWJ, Cremers FPM, Qamar R. Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome. Mol Vis 2013; 19:644-53. [PMID: 23559858 PMCID: PMC3616519] [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: 07/13/2012] [Accepted: 03/19/2013] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To determine the genetic cause of Bardet-Biedl syndrome (BBS) in two consanguineous Pakistani families. METHODS Clinical characterization of the affected individuals in both families was performed with ophthalmic examination, electroretinography, electrocardiography, and liver and renal profiling. Seventeen genes are known to be associated with BBS, so exome sequencing was preferred over candidate gene sequencing. One affected individual from both families was selected for exome sequencing. Segregation of the identified variants was confirmed with Sanger sequencing. RESULTS Retinitis pigmentosa, obesity, and learning difficulties were present in the affected individuals in both families. In family A, a sixth finger (polydactyly) of the proband's sister was removed by a surgical operation leaving a scar on the little finger. Polydactyly was also present in both affected individuals from family B. All diagnostic symptoms were characteristic of BBS in both families. In both affected individuals from family A, exome sequencing identified a novel homozygous mutation (c.47+1G>T) in BBS1 that inactivates the splice donor site at the end of exon 1. In family B, a previously reported mutation, c.442G>A; p.(Asp148Asn), was detected. CONCLUSIONS Exome sequencing is an efficient and cost-effective technique for identifying mutations in genetically heterogeneous diseases. In addition, intrafamilial phenotypic variability in family A argues for the modifying effect of other still unknown modifier alleles.
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Affiliation(s)
- Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Muhammad Imran Khan
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ali Tayyab
- Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Sulman Jaffar
- Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan,Department of Ophthalmology, Shifa International Hospital, Islamabad, Pakistan
| | - Ahmed Sadeque
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Humaira Ayub
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Nasir Mahmood Abbasi
- Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Moeen Riaz
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Shazia Micheal
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
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Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V. Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures. PLoS One 2012; 7:e43799. [PMID: 22952768 PMCID: PMC3430670 DOI: 10.1371/journal.pone.0043799] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/26/2012] [Indexed: 11/20/2022] Open
Abstract
Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.
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Affiliation(s)
- Danilo Licastro
- Cluster in Biomedicine (CBM) scrl - Genomics, Area Science Park, Basovizza, Trieste, Italy
| | | | - Ivana Peluso
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Kornelia Neveling
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Nienke Wieskamp
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Rossella Rispoli
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Diego Vozzi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | | | - Angela D'Eustacchio
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | | | - Francesca D'Amico
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Carmela Ziviello
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Francesca Simonelli
- Dipartimento di Oftalmologia, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Antonella Fabretto
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | - Hans Scheffer
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
- * E-mail: (PG); (SB); (VN)
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
- * E-mail: (PG); (SB); (VN)
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
- * E-mail: (PG); (SB); (VN)
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Kleefstra T, Kramer J, Neveling K, Willemsen M, Koemans T, Vissers L, Wissink-Lindhout W, Fenckova M, van den Akker W, Kasri N, Nillesen W, Prescott T, Clark R, Devriendt K, van Reeuwijk J, de Brouwer A, Gilissen C, Zhou H, Brunner H, Veltman J, Schenck A, van Bokhoven H. Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. Am J Hum Genet 2012; 91:73-82. [PMID: 22726846 DOI: 10.1016/j.ajhg.2012.05.003] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/10/2012] [Accepted: 05/14/2012] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) disorders are genetically and phenotypically highly heterogeneous and present a major challenge in clinical genetics and medicine. Although many genes involved in ID have been identified, the etiology is unknown in most affected individuals. Moreover, the function of most genes associated with ID remains poorly characterized. Evidence is accumulating that the control of gene transcription through epigenetic modification of chromatin structure in neurons has an important role in cognitive processes and in the etiology of ID. However, our understanding of the key molecular players and mechanisms in this process is highly fragmentary. Here, we identify a chromatin-modification module that underlies a recognizable form of ID, the Kleefstra syndrome phenotypic spectrum (KSS). In a cohort of KSS individuals without mutations in EHMT1 (the only gene known to be disrupted in KSS until now), we identified de novo mutations in four genes, MBD5, MLL3, SMARCB1, and NR1I3, all of which encode epigenetic regulators. Using Drosophila, we demonstrate that MBD5, MLL3, and NR1I3 cooperate with EHMT1, whereas SMARCB1 is known to directly interact with MLL3. We propose a highly conserved epigenetic network that underlies cognition in health and disease. This network should allow the design of strategies to treat the growing group of ID pathologies that are caused by epigenetic defects.
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Ajmal M, Khan MI, Neveling K, Khan YM, Ali SHB, Ahmed W, Iqbal MS, Azam M, den Hollander AI, Collin RW, Qamar R, Cremers FP. Novel mutations in RDH5 cause fundus albipunctatus in two consanguineous Pakistani families. Mol Vis 2012; 18:1558-71. [PMID: 22736946 PMCID: PMC3380946] [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: 03/06/2012] [Accepted: 06/10/2012] [Indexed: 11/16/2022] Open
Abstract
PURPOSE To identify the underlying genetic causes of fundus albipunctatus (FA), a rare form of congenital stationary night blindness that is characterized by the presence of white dots in the midperiphery of the retina and delayed dark adaptation, in Pakistan. METHODS Two families with FA were identified by fundus examination, and genome-wide single nucleotide polymorphism genotyping was performed for two individuals from family A and six individuals from family B. Genotyping data were subsequently used to identify the identical homozygous regions present in the affected individuals of both families using the online homozygosity mapping tool Homozygosity Mapper. Candidate genes selected from the homozygous regions were sequenced. RESULTS Three identical homozygous regions were identified in affected persons of family A (on chromosomes 8, 10, and 12), whereas a single shared homozygous region on chromosome 12 was found in family B. In both families, the homozygous region on chromosome 12 harbored the retinol dehydrogenase 5 (RDH5) gene, in which mutations are known to be causative of FA. RDH5 sequence analysis revealed a novel five base pair deletion, c.913_917delGTGCT (p.Val305Hisfs*29), in family A, and a novel missense mutation, c.758T>G (p.Met253Arg), in family B. CONCLUSIONS We identified two novel disease-causing RDH5 mutations in Pakistani families with FA, which will improve diagnosis and genetic counseling, and may even lead to treatment of this disease in these families.
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Affiliation(s)
- Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Shifa College of Medicine, Islamabad, Pakistan
| | - Muhammad Imran Khan
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Institute for Genetic and Metabolic Disorders, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Yar Muhammad Khan
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Chemistry, University of Science and Technology, Bannu-28100, Pakistan
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Waqas Ahmed
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | | | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Anneke I. den Hollander
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Shifa College of Medicine, Islamabad, Pakistan
| | - Frans P.M. Cremers
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Abstract
ZusammenfassungNeueste Sequenziertechnologien („next-generation sequencing“) erlauben die gleichzeitige Sequenzierung aller proteinkodierender Sequenzen, das sog. Exom. Die Identifizierung der jeweiligen pathogenen Mutation unter den Tausenden detektierten Varianten stellt dabei eine große Herausforderung dar, und neue Strategien für die Priorisierung von Varianten sind unerlässlich. Die jeweilige Wahl einer Strategie ist dabei von verschiedenen Faktoren abhängig, wie z. B. dem Vorhandensein gut charakterisierter Patienten und deren Familien, von der Art der Vererbung, der Schwere der Krankheit sowie deren Frequenz in der allgemeinen Bevölkerung. In dem vorliegenden Übersichtsartikel diskutieren wir die heute gebräuchlichen Strategien zur Identifizierung von neuen Krankheitsgenen mittels Exom-Sequenzierung und beschreiben die Lehren der ersten Exom-Studien. Wir glauben, dass die Sequenzierung von Exomen in den folgenden Jahren die am häufigsten angewandte Methode zur Identifizierung von Krankheitsgenen sein wird und dabei gleichzeitig auch ein großes diagnostisches Potenzial aufweist.
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Affiliation(s)
- K. Neveling
- Aff1_313 grid.10417.33 0000000404449382 Department of Human Genetics Radboud University Medical Centre Nijmegen Geert Grooteplein 10 6500HB Nijmegen Niederlande
| | - A. Hoischen
- Aff1_313 grid.10417.33 0000000404449382 Department of Human Genetics Radboud University Medical Centre Nijmegen Geert Grooteplein 10 6500HB Nijmegen Niederlande
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Neveling K, Collin RWJ, Gilissen C, van Huet RAC, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FPM, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat 2012; 33:963-72. [PMID: 22334370 PMCID: PMC3490376 DOI: 10.1002/humu.22045] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [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: 10/19/2011] [Accepted: 01/18/2012] [Indexed: 01/07/2023]
Abstract
Molecular diagnostics for patients with retinitis pigmentosa (RP) has been hampered by extreme genetic and clinical heterogeneity, with 52 causative genes known to date. Here, we developed a comprehensive next-generation sequencing (NGS) approach for the clinical molecular diagnostics of RP. All known inherited retinal disease genes (n = 111) were captured and simultaneously analyzed using NGS in 100 RP patients without a molecular diagnosis. A systematic data analysis pipeline was developed and validated to prioritize and predict the pathogenicity of all genetic variants identified in each patient, which enabled us to reduce the number of potential pathogenic variants from approximately 1,200 to zero to nine per patient. Subsequent segregation analysis and in silico predictions of pathogenicity resulted in a molecular diagnosis in 36 RP patients, comprising 27 recessive, six dominant, and three X-linked cases. Intriguingly, De novo mutations were present in at least three out of 28 isolated cases with causative mutations. This study demonstrates the enormous potential and clinical utility of NGS in molecular diagnosis of genetically heterogeneous diseases such as RP. De novo dominant mutations appear to play a significant role in patients with isolated RP, having major implications for genetic counselling.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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50
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Iqbal Z, Neveling K, Razzaq A, Shahzad M, Zahoor MY, Qasim M, Gilissen C, Wieskamp N, Kwint MP, Gijsen S, de Brouwer APM, Veltman JA, Riazuddin S, van Bokhoven H. Targeted next generation sequencing reveals a novel intragenic deletion of the TPO gene in a family with intellectual disability. Arch Med Res 2012; 43:312-6. [PMID: 22387573 DOI: 10.1016/j.arcmed.2012.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 08/19/2011] [Accepted: 01/18/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUNDS AND AIMS Next generation sequencing (NGS) approaches have revolutionized the identification of mutations underlying genetic disorders. This technology is particularly useful for the identification of mutations in known and new genes for conditions with extensive genetic heterogeneity. In the present study we investigated a consanguineous Pakistani family with intellectual disability (ID). METHODS Genotyping was carried out using 250k and 6k SNP microarrays in order to perform homozygosity mapping and copy number variation (CNV) analysis. Targeted NGS was performed to identify the genetic defect in this family. qPCR was performed to validate and confirm the NGS result. RESULTS Homozygosity mapping positioned the causative defect on chromosome 2p25.3-p25.2. Subsequent targeted NGS revealed an intragenic deletion of five exons of the gene TPO. CONCLUSIONS NGS is a powerful method to uncover submicroscopic structural variations. This result demonstrates that an unbiased screening approach such as NGS can help to identify even unexpected disease-causing mutations.
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Affiliation(s)
- Zafar Iqbal
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, The Netherlands
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