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Saacks NA, Eales J, Spracklen TF, Aldersley T, Human P, Verryn M, Lawrenson J, Cupido B, Comitis G, De Decker R, Fourie B, Swanson L, Joachim A, Brooks A, Ramesar R, Shaboodien G, Keavney BD, Zühlke LJ. Investigation of Copy Number Variation in South African Patients With Congenital Heart Defects. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003510. [PMID: 36205932 PMCID: PMC9770125 DOI: 10.1161/circgen.121.003510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/27/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is a leading non-infectious cause of pediatric morbidity and mortality worldwide. Although the etiology of CHD is poorly understood, genetic factors including copy number variants (CNVs) contribute to the risk of CHD in individuals of European ancestry. The presence of rare CNVs in African CHD populations is unknown. This study aimed to identify pathogenic and likely pathogenic CNVs in South African patients with CHD. METHODS Genotyping was performed on 90 patients with nonsyndromic CHD using the Affymetrix CytoScan HD platform. These data were used to identify large, rare CNVs in known CHD-associated genes and candidate genes. RESULTS We identified eight CNVs overlapping known CHD-associated genes (GATA4, CRKL, TBX1, FLT4, B3GAT3, NSD1) in six patients. The analysis also revealed CNVs encompassing five candidate genes likely to play a role in the development of CHD (DGCR8, KDM2A, JARID2, FSTL1, CYFIP1) in five patients. One patient was found to have 47, XXY karyotype. We report a total discovery yield of 6.7%, with 5.6% of the cohort carrying pathogenic or likely pathogenic CNVs expected to cause the observed phenotypes. CONCLUSIONS In this study, we show that chromosomal microarray is an effective technique for identifying CNVs in African patients diagnosed with CHD and have demonstrated results similar to previous CHD genetic studies in Europeans. Novel potential CHD genes were also identified, indicating the value of genetic studies of CHD in ancestrally diverse populations.
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Affiliation(s)
- Nicole A. Saacks
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - James Eales
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom (J.E., B.D.K.)
| | - Timothy F. Spracklen
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
| | - Thomas Aldersley
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Paul Human
- Chris Barnard Division of Cardiothoracic Surgery, Department of Medicine, Faculty of Health Sciences (P.H., A.B.)
| | - Mark Verryn
- Cardiovascular Genetics Laboratory, Hatter Institute for Cardiovascular Research in Africa (M.V., G.S.)
| | - John Lawrenson
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health, University of Stellenbosch, Cape Town, South Africa (J.L., B.F.)
| | - Blanche Cupido
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences (B.C., L.J.Z.)
| | - George Comitis
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Rik De Decker
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Barend Fourie
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health, University of Stellenbosch, Cape Town, South Africa (J.L., B.F.)
| | - Lenise Swanson
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Alexia Joachim
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Andre Brooks
- Chris Barnard Division of Cardiothoracic Surgery, Department of Medicine, Faculty of Health Sciences (P.H., A.B.)
| | - Raj Ramesar
- MRC Genomic & Precision Medicine Research Unit, Division of Human Genetics, Dept of Pathology, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa (R.R.)
| | - Gasnat Shaboodien
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
- Cardiovascular Genetics Laboratory, Hatter Institute for Cardiovascular Research in Africa (M.V., G.S.)
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom (J.E., B.D.K.)
| | - Liesl J. Zühlke
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences (B.C., L.J.Z.)
- South African Medical Research Council, Cape Town (L.J.Z.)
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2
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Bando H, Urai S, Kanie K, Sasaki Y, Yamamoto M, Fukuoka H, Iguchi G, Camper SA. Novel genes and variants associated with congenital pituitary hormone deficiency in the era of next-generation sequencing. Front Endocrinol (Lausanne) 2022; 13:1008306. [PMID: 36237189 PMCID: PMC9551393 DOI: 10.3389/fendo.2022.1008306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/09/2022] [Indexed: 01/07/2023] Open
Abstract
Combined pituitary hormone deficiency (CPHD) is not a rare disorder, with a frequency of approximately 1 case per 4,000 live births. However, in most cases, a genetic diagnosis is not available. Furthermore, the diagnosis is challenging because no clear correlation exists between the pituitary hormones affected and the gene(s) responsible for the disorder. Next-generation sequencing (NGS) has recently been widely used to identify novel genes that cause (or putatively cause) CPHD. This review outlines causative genes for CPHD that have been newly reported in recent years. Moreover, novel variants of known CPHD-related genes (POU1F1 and GH1 genes) that contribute to CPHD through unique mechanisms are also discussed in this review. From a clinical perspective, variants in some of the recently identified causative genes result in extra-pituitary phenotypes. Clinical research on the related symptoms and basic research on pituitary formation may help in inferring the causative gene(s) of CPHD. Future NGS analysis of a large number of CPHD cases may reveal new genes related to pituitary development. Clarifying the causative genes of CPHD may help to understand the process of pituitary development. We hope that future innovations will lead to the identification of genes responsible for CPHD and pituitary development.
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Affiliation(s)
- Hironori Bando
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- *Correspondence: Hironori Bando,
| | - Shin Urai
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Keitaro Kanie
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Yuriko Sasaki
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Masaaki Yamamoto
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Hidenori Fukuoka
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Genzo Iguchi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan
- Medical Center for Student Health, Kobe University, Kobe, Japan
| | - Sally A. Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
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3
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Dubail J, Cormier-Daire V. Chondrodysplasias With Multiple Dislocations Caused by Defects in Glycosaminoglycan Synthesis. Front Genet 2021; 12:642097. [PMID: 34220933 PMCID: PMC8242584 DOI: 10.3389/fgene.2021.642097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Chondrodysplasias with multiple dislocations form a group of severe disorders characterized by joint laxity and multiple dislocations, severe short stature of pre- and post-natal onset, hand anomalies, and/or vertebral anomalies. The majority of chondrodysplasias with multiple dislocations have been associated with mutations in genes encoding glycosyltransferases, sulfotransferases, and transporters implicated in the synthesis or sulfation of glycosaminoglycans, long and unbranched polysaccharides composed of repeated disaccharide bond to protein core of proteoglycan. Glycosaminoglycan biosynthesis is a tightly regulated process that occurs mainly in the Golgi and that requires the coordinated action of numerous enzymes and transporters as well as an adequate Golgi environment. Any disturbances of this chain of reactions will lead to the incapacity of a cell to construct correct glycanic chains. This review focuses on genetic and glycobiological studies of chondrodysplasias with multiple dislocations associated with glycosaminoglycan biosynthesis defects and related animal models. Strong comprehension of the molecular mechanisms leading to those disorders, mostly through extensive phenotypic analyses of in vitro and/or in vivo models, is essential for the development of novel biomarkers for clinical screenings and innovative therapeutics for these diseases.
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Affiliation(s)
- Johanne Dubail
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Valérie Cormier-Daire
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France.,Service de Génétique Clinique, Centre de Référence Pour Les Maladies Osseuses Constitutionnelles, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
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4
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Byrne AB, Mizumoto S, Arts P, Yap P, Feng J, Schreiber AW, Babic M, King-Smith SL, Barnett CP, Moore L, Sugahara K, Mutlu-Albayrak H, Nishimura G, Liebelt JE, Yamada S, Savarirayan R, Scott HS. Pseudodiastrophic dysplasia expands the known phenotypic spectrum of defects in proteoglycan biosynthesis. J Med Genet 2020; 57:454-460. [PMID: 31988067 PMCID: PMC7361035 DOI: 10.1136/jmedgenet-2019-106700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/09/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023]
Abstract
Background Pseudodiastrophic dysplasia (PDD) is a severe skeletal dysplasia associated with prenatal manifestation and early lethality. Clinically, PDD is classified as a ‘dysplasia with multiple joint dislocations’; however, the molecular aetiology of the disorder is currently unknown. Methods Whole exome sequencing (WES) was performed on three patients from two unrelated families, clinically diagnosed with PDD, in order to identify the underlying genetic cause. The functional effects of the identified variants were characterised using primary cells and human cell-based overexpression assays. Results WES resulted in the identification of biallelic variants in the established skeletal dysplasia genes, B3GAT3 (family 1) and CANT1 (family 2). Mutations in these genes have previously been reported to cause ‘multiple joint dislocations, short stature, and craniofacial dysmorphism with or without congenital heart defects’ (‘JDSCD’; B3GAT3) and Desbuquois dysplasia 1 (CANT1), disorders in the same nosological group as PDD. Follow-up of the B3GAT3 variants demonstrated significantly reduced B3GAT3/GlcAT-I expression. Downstream in vitro functional analysis revealed abolished biosynthesis of glycosaminoglycan side chains on proteoglycans. Functional evaluation of the CANT1 variant showed impaired nucleotidase activity, which results in inhibition of glycosaminoglycan synthesis through accumulation of uridine diphosphate. Conclusion For the families described in this study, the PDD phenotype was caused by mutations in the known skeletal dysplasia genes B3GAT3 and CANT1, demonstrating the advantage of genomic analyses in delineating the molecular diagnosis of skeletal dysplasias. This finding expands the phenotypic spectrum of B3GAT3-related and CANT1-related skeletal dysplasias to include PDD and highlights the significant phenotypic overlap of conditions within the proteoglycan biosynthesis pathway.
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Affiliation(s)
- Alicia B Byrne
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan.,Research Center for Pathogenesis of Intractable Diseases, Meijo University, Nagoya, Japan.,Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Patrick Yap
- Victorian Clinical Genetics Service, Royal Children's Hospital, Melbourne, Victoria, Australia.,Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jinghua Feng
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Andreas W Schreiber
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Sarah L King-Smith
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia.,School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lynette Moore
- School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia.,Department of Surgical Pathology, Women's and Children's Hospital, SA Pathology, North Adelaide, South Australia, Australia
| | - Kazuyuki Sugahara
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Hatice Mutlu-Albayrak
- Department of Pediatric Genetics, Cengiz Gökcek Obstetrics and Children's Hospital, Gaziantep, Turkey
| | - Gen Nishimura
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Jan E Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan.,Research Center for Pathogenesis of Intractable Diseases, Meijo University, Nagoya, Japan
| | - Ravi Savarirayan
- Victorian Clinical Genetics Service, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia .,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia.,School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
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Colman M, Van Damme T, Steichen-Gersdorf E, Laccone F, Nampoothiri S, Syx D, Guillemyn B, Symoens S, Malfait F. The clinical and mutational spectrum of B3GAT3 linkeropathy: two case reports and literature review. Orphanet J Rare Dis 2019; 14:138. [PMID: 31196143 PMCID: PMC6567438 DOI: 10.1186/s13023-019-1110-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/04/2019] [Indexed: 01/07/2023] Open
Abstract
Background Proteoglycans are large and structurally complex macromolecules which can be found in abundancy in the extracellular matrix and on the surface of all animal cells. Mutations in the genes encoding the enzymes responsible for the formation of the tetrasaccharide linker region between the proteoglycan core protein and the glycosaminoglycan side chains lead to a spectrum of severe and overlapping autosomal recessive connective tissue disorders, collectively coined the ‘glycosaminoglycan linkeropathies’. Results We report the clinical findings of two novel patients with a complex linkeropathy due to biallelic mutations in B3GAT3, the gene that encodes glucuronosyltransferase I, which catalyzes the addition of the ultimate saccharide to the linker region. We identified a previously reported c.667G > A missense mutation and an unreported homozygous c.416C > T missense mutation. We also performed a genotype and phenotype-oriented literature overview of all hitherto reported patients harbouring B3GAT3 mutations. A total of 23 patients from 10 families harbouring bi-allelic mutations and one patient with a heterozygeous splice-site mutation in B3GAT3 have been reported. They all display a complex phenotype characterized by consistent presence of skeletal dysplasia (including short stature, kyphosis, scoliosis and deformity of the long bones), facial dysmorphology, and spatulate distal phalanges. More variably present are cardiac defects, joint hypermobility, joint dislocations/contractures and fractures. Seven different B3GAT3 mutations have been reported, and although the number of patients is still limited, some phenotype-genotype correlations start to emerge. The more severe phenotypes seem to have mutations located in the substrate acceptor subdomain of the catalytic domain of the glucuronosyltransferase I protein while more mildly affected phenotypes seem to have mutations in the NTP-sugar donor substrate binding subdomain. Conclusions Loss-of-function mutations in B3GAT3 are associated with a complex connective tissue phenotype characterized by disproportionate short stature, skeletal dysplasia, facial dysmorphism, spatulate distal phalanges and -to a lesser extent- joint contractures, joint hypermobility with dislocations, cardiac defects and bone fragility. Based on the limited number of reported patients, some genotype-phenotype correlations start to emerge.
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Affiliation(s)
- Marlies Colman
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Tim Van Damme
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | | | | | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Kerala, India
| | - Delfien Syx
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Brecht Guillemyn
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University and Ghent University Hospital, 0K5, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
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Abstract
In 1993, Jabs et al. were the first to describe a genetic origin of craniosynostosis. Since this discovery, the genetic causes of the most common syndromes have been described. In 2015, a total of 57 human genes were reported for which there had been evidence that mutations were causally related to craniosynostosis. Facilitated by rapid technological developments, many others have been identified since then. Reviewing the literature, we characterize the most common craniosynostosis syndromes followed by a description of the novel causes that were identified between January 2015 and December 2017.
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Affiliation(s)
- Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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