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Baardman R, Lemmink HH, Yenamandra VK, Commandeur-Jan SZ, Viel M, Kooi KA, Diercks GFH, Meijer R, van Geel M, Scheffer H, Sinke RJ, Sikkema-Raddatz B, Bolling MC, van den Akker PC. Evolution of genome diagnostics in epidermolysis bullosa: Unveiling the power of next-generation sequencing. J Eur Acad Dermatol Venereol 2024. [PMID: 38465480 DOI: 10.1111/jdv.19938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Genome diagnostics is considered gold standard diagnostics for epidermolysis bullosa (EB), a phenotypically and genetically heterogeneous group of rare disorders characterized by blistering and wounding of mucocutaneous tissues. EB is caused by pathogenic variants in genes encoding proteins of the dermo-epidermal junction. Accurate genetic diagnosis of EB is crucial for prognostication, counselling and precision-medicine. Genome diagnostics for EB started in 1991 with the introduction of Sanger sequencing (SS), analysing one gene at a time. In 2013, SS was superseded by next-generation sequencing (NGS), that allow for high-throughput sequencing of multiple genes in parallel. Several studies have shown a beneficial role for NGS in EB diagnostics, but its true benefit has not been quantified. OBJECTIVES To determine the benefit of NGS in EB by systematically evaluating the performance of different genome diagnostics used over time based on robust data from the Dutch EB Registry. METHODS The diagnostic performances of SS and NGS were systematically evaluated in a retrospective observational study including all index cases with a clinical diagnosis of EB in whom genome diagnostics was performed between 01 January 1994 and 01 January 2022 (n = 308), registered at the Dutch EB Expertise Centre. RESULTS Over time, a genetic diagnosis was made in 289/308 (94%) EB cases. The diagnostic yield increased from 89% (SS) to 95% (NGS). Most importantly, NGS significantly reduced diagnostic turnaround time (39 days vs. 211 days, p < 0.001). The likelihood of detecting variants of uncertain significance and additional findings increased from 5% and 1% (SS) to 22% and 13% (NGS) respectively. CONCLUSIONS Our study quantifies the benefit of NGS-based methods and demonstrate they have had a major impact on EB diagnostics through an increased diagnostic yield and a dramatically decreased turnaround time (39 days). Although our diagnostic yield is high (95%), further improvement of genome diagnostics is urgently needed to provide a genetic diagnosis in all EB patients.
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Affiliation(s)
- R Baardman
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H H Lemmink
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - V K Yenamandra
- Academy of Scientific and Innovative Research South Campus, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - S Z Commandeur-Jan
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Viel
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - K A Kooi
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - G F H Diercks
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - R Meijer
- Department of Genetics, University Medical Center Nijmegen, University of Nijmegen, Nijmegen, The Netherlands
| | - M van Geel
- Department of Genetics, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands
| | - H Scheffer
- Department of Genetics, University Medical Center Nijmegen, University of Nijmegen, Nijmegen, The Netherlands
| | - R J Sinke
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - B Sikkema-Raddatz
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M C Bolling
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - P C van den Akker
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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2
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Olde Keizer RACM, Marouane A, Kerstjens-Frederikse WS, Deden AC, Lichtenbelt KD, Jonckers T, Vervoorn M, Vreeburg M, Henneman L, de Vries LS, Sinke RJ, Pfundt R, Stevens SJC, Andriessen P, van Lingen RA, Nelen M, Scheffer H, Stemkens D, Oosterwijk C, van Amstel HKP, de Boode WP, van Zelst-Stams WAG, Frederix GWJ, Vissers LELM. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands. Eur J Pediatr 2023:10.1007/s00431-023-04909-1. [PMID: 36997769 PMCID: PMC10257607 DOI: 10.1007/s00431-023-04909-1] [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] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 04/01/2023]
Abstract
The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests. • Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.
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Grants
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 779257 Horizon 2020 Framework Programme
- 779257 Horizon 2020 Framework Programme
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Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - A Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - Tinneke Jonckers
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Marieke Vervoorn
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Linda S de Vries
- Department of Neonatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Peter Andriessen
- Department of Pediatrics, Máxima Medical Center, Veldhoven, Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Daphne Stemkens
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | - Cor Oosterwijk
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | | | - Willem P de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children's Hospital, Nijmegen, Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands.
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.
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3
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Vansenne F, Fock JM, Stolte-Dijkstra I, Meiners LC, van den Boogaard MJH, Jaeger B, Boven L, Vos YJ, Sinke RJ, Verbeek DS. Phenotypic expansion of EGP5-related Vici syndrome: 15 Dutch patients carrying a founder variant. Eur J Paediatr Neurol 2022; 41:91-98. [PMID: 36410285 DOI: 10.1016/j.ejpn.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Vici syndrome (OMIM 242840) is a very rare autosomal recessive multisystem disorder first described in 1988. In 2013, bi-allelic loss-of-function mutations in EPG5 were reported to cause Vici syndrome. Five principal diagnostic features of Vici syndrome have been proposed: agenesis of the corpus callosum, cataracts, cardiomyopathy, hypopigmentation, and combined immunodeficiency. We identified 15 patients carrying a homozygous founder missense variant in EPG5 who all exhibit a less severe clinical phenotype than classic Vici syndrome. All 15 show typical brain abnormalities on MRI. The homozygous founder variant in EPG5 they carry results in a shorter in-frame transcript and truncated, but likely still residual, EPG5 protein. We speculate that the residual EPG5 protein explains their attenuated phenotype, which is consistent with two previous observations that low expression of EPG5 can lead to an attenuated Vici syndrome phenotype. We propose renaming this condition EPG5-related neurodevelopmental disorder to emphasize the clinical variability of patients with bi-allelic mutations in EPG5.
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Affiliation(s)
- Fleur Vansenne
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Johanna M Fock
- Department of Pediatric Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Irene Stolte-Dijkstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Linda C Meiners
- Department of Radiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Bregje Jaeger
- Department of Pediatric Neurology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ludolf Boven
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yvonne J Vos
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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4
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Veldman A, Kiewiet MBG, Heiner-Fokkema MR, Nelen MR, Sinke RJ, Sikkema-Raddatz B, Voorhoeve E, Westra D, Dollé MET, Schielen PCJI, van Spronsen FJ. Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead. Int J Neonatal Screen 2022; 8:ijns8010017. [PMID: 35323196 PMCID: PMC8949100 DOI: 10.3390/ijns8010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe the aim and set-up of the NGS-first for the NBS (NGSf4NBS) project, which will proceed in three steps. In Step 1, we will identify IMDs eligible for NGS-first testing, based on treatability. In Step 2, we will investigate the feasibility, limitations and comparability of different technical NGS approaches and analysis workflows for NBS, eventually aiming to develop a rapid NGS-based workflow. Finally, in Step 3, we will prepare for the incorporation of this workflow into the existing Dutch NBS program and propose a protocol for referral of a child after a positive NGS test result. The results of this study will be the basis for an additional analytical route within NBS that will be further studied for its applicability within the NBS program, e.g., regarding the ethical, legal, financial and social implications.
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Affiliation(s)
- Abigail Veldman
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Correspondence: (A.V.); (M.B.G.K.)
| | - Mensiena B. G. Kiewiet
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
- Correspondence: (A.V.); (M.B.G.K.)
| | - Margaretha Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marcel R. Nelen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Richard J. Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Els Voorhoeve
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Peter C. J. I. Schielen
- Centre for Population Screening, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands;
| | - Francjan J. van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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5
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Zhang Z, van Dijk F, de Klein N, van Gijn ME, Franke LH, Sinke RJ, Swertz MA, van der Velde KJ. Feasibility of predicting allele specific expression from DNA sequencing using machine learning. Sci Rep 2021; 11:10606. [PMID: 34012022 PMCID: PMC8134421 DOI: 10.1038/s41598-021-89904-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/04/2021] [Indexed: 11/09/2022] Open
Abstract
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. However, genome diagnostics is based on DNA sequencing and therefore neglects gene expression regulation such as ASE. To take advantage of ASE in absence of RNA sequencing, it must be predicted using only DNA variation. We have constructed ASE models from BIOS (n = 3432) and GTEx (n = 369) that predict ASE using DNA features. These models are highly reproducible and comprise many different feature types, highlighting the complex regulation that underlies ASE. We applied the BIOS-trained model to population variants in three genes in which ASE plays a clinically relevant role: BRCA2, RET and NF1. This resulted in predicted ASE effects for 27 variants, of which 10 were known pathogenic variants. We demonstrated that ASE can be predicted from DNA features using machine learning. Future efforts may improve sensitivity and translate these models into a new type of genome diagnostic tool that prioritizes candidate pathogenic variants or regulators thereof for follow-up validation by RNA sequencing. All used code and machine learning models are available at GitHub and Zenodo.
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Affiliation(s)
- Zhenhua Zhang
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Freerk van Dijk
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Prinses Maxima Center for Child Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Niek de Klein
- Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Lude H Franke
- Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - K Joeri van der Velde
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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6
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Alimohamed MZ, Johansson LF, Posafalvi A, Boven LG, van Dijk KK, Walters L, Vos YJ, Westers H, Hoedemaekers YM, Sinke RJ, Sijmons RH, Sikkema-Raddatz B, Jongbloed JDH, van der Zwaag PA. Diagnostic yield of targeted next generation sequencing in 2002 Dutch cardiomyopathy patients. Int J Cardiol 2021; 332:99-104. [PMID: 33662488 DOI: 10.1016/j.ijcard.2021.02.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/13/2021] [Accepted: 02/17/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly used for clinical evaluation of cardiomyopathy patients as it allows for simultaneous screening of multiple cardiomyopathy-associated genes. Adding copy number variant (CNV) analysis of NGS data is not routine yet and may contribute to the diagnostic yield. OBJECTIVES Determine the diagnostic yield of our targeted NGS gene panel in routine clinical diagnostics of Dutch cardiomyopathy patients and explore the impact of exon CNVs on diagnostic yield. METHODS Patients (N = 2002) referred for clinical genetic analysis underwent diagnostic testing of 55-61 genes associated with cardiomyopathies. Samples were analyzed and evaluated for single nucleotide variants (SNVs), indels and CNVs. CNVs identified in the NGS data and suspected of being pathogenic based on type, size and location were confirmed by additional molecular tests. RESULTS A (likely) pathogenic (L)P variant was detected in 22.7% of patients, including 3 with CNVs and 25 where a variant was identified in a gene currently not associated with the patient's cardiomyopathy subtype. Only 15 out of 2002 patients (0.8%) were found to carry two (L)P variants. CONCLUSION The yield of routine clinical diagnostics of cardiomyopathies was relatively low when compared to literature. This is likely due to the fact that our study reports the outcome of patients in daily routine diagnostics, therefore also including patients not fully fulfilling (subtype specific) cardiomyopathy criteria. This may also explain why (L)P variants were identified in genes not associated with the reported subtype. The added value of CNV analysis was shown to be limited but not negligible.
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Affiliation(s)
- Mohamed Z Alimohamed
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands.
| | - Lennart F Johansson
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Anna Posafalvi
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Ludolf G Boven
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Krista K van Dijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Lisa Walters
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Yvonne J Vos
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Helga Westers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Yvonne M Hoedemaekers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Rolf H Sijmons
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Jan D H Jongbloed
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands.
| | - Paul A van der Zwaag
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
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7
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Huang M, Nibbeling EAR, Lagrand TJ, Souza IA, Groen JL, Gandini MA, Zhang FX, Koelman JHTM, Adir N, Sinke RJ, Zamponi GW, Tijssen MAJ, Verbeek DS. Rare functional missense variants in CACNA1H: What can we learn from Writer's cramp? Mol Brain 2021; 14:18. [PMID: 33478561 PMCID: PMC7819179 DOI: 10.1186/s13041-021-00736-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022] Open
Abstract
Writer's cramp (WC) is a task-specific focal dystonia that occurs selectively in the hand and arm during writing. Previous studies have shown a role for genetics in the pathology of task-specific focal dystonia. However, to date, no causal gene has been reported for task-specific focal dystonia, including WC. In this study, we investigated the genetic background of a large Dutch family with autosomal dominant‒inherited WC that was negative for mutations in known dystonia genes. Whole exome sequencing identified 4 rare variants of unknown significance that segregated in the family. One candidate gene was selected for follow-up, Calcium Voltage-Gated Channel Subunit Alpha1 H, CACNA1H, due to its links with the known dystonia gene Potassium Channel Tetramerization Domain Containing 17, KCTD17, and with paroxysmal movement disorders. Targeted resequencing of CACNA1H in 82 WC cases identified another rare, putative damaging variant in a familial WC case that did not segregate. Using structural modelling and functional studies in vitro, we show that both the segregating p.Arg481Cys variant and the non-segregating p.Glu1881Lys variant very likely cause structural changes to the Cav3.2 protein and lead to similar gains of function, as seen in an accelerated recovery from inactivation. Both mutant channels are thus available for re-activation earlier, which may lead to an increase in intracellular calcium and increased neuronal excitability. Overall, we conclude that rare functional variants in CACNA1H need to be interpreted very carefully, and additional studies are needed to prove that the p.Arg481Cys variant is the cause of WC in the large Dutch family.
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Affiliation(s)
- Miaozhen Huang
- Department of Genetics, University Medical Center Groningen, University of Groningen, P.O. box 30 001, 9700 RB, Groningen, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tjerk J Lagrand
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ivana A Souza
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Justus L Groen
- Department of Neurosurgery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maria A Gandini
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Fang-Xiong Zhang
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Johannes H T M Koelman
- Department of Neurology and Clinical Neurophysiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion, Israel
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, P.O. box 30 001, 9700 RB, Groningen, The Netherlands
| | - Gerald W Zamponi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marina A J Tijssen
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, P.O. box 30 001, 9700 RB, Groningen, The Netherlands.
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8
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Li S, van der Velde KJ, de Ridder D, van Dijk ADJ, Soudis D, Zwerwer LR, Deelen P, Hendriksen D, Charbon B, van Gijn ME, Abbott K, Sikkema-Raddatz B, van Diemen CC, Kerstjens-Frederikse WS, Sinke RJ, Swertz MA. CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations. Genome Med 2020; 12:75. [PMID: 32831124 PMCID: PMC7446154 DOI: 10.1186/s13073-020-00775-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 11/25/2019] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual classification by experts. Here we introduce CAPICE, a new machine-learning-based method for prioritizing pathogenic variants, including SNVs and short InDels. CAPICE outperforms the best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily added to diagnostic pipelines as pre-computed score file or command-line software, or using online MOLGENIS web service with API. Download CAPICE for free and open-source (LGPLv3) at https://github.com/molgenis/capice .
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Affiliation(s)
- Shuang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - K Joeri van der Velde
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands
- Biometris, Wageningen University & Research, Wageningen, the Netherlands
| | - Dimitrios Soudis
- Donald Smits Center for Information and Technology, University of Groningen, Groningen, the Netherlands
| | - Leslie R Zwerwer
- Donald Smits Center for Information and Technology, University of Groningen, Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dennis Hendriksen
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bart Charbon
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kristin Abbott
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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9
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Bremer J, van der Heijden EH, Eichhorn DS, Meijer R, Lemmink HH, Scheffer H, Sinke RJ, Jonkman MF, Pasmooij AMG, Van den Akker PC. Natural Exon Skipping Sets the Stage for Exon Skipping as Therapy for Dystrophic Epidermolysis Bullosa. Mol Ther Nucleic Acids 2019; 18:465-475. [PMID: 31670143 PMCID: PMC6831832 DOI: 10.1016/j.omtn.2019.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 05/16/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 02/04/2023]
Abstract
Dystrophic epidermolysis bullosa (DEB) is a devastating blistering disease affecting skin and mucous membranes. It is caused by pathogenic variants in the COL7A1 gene encoding type VII collagen, and can be inherited dominantly or recessively. Recently, promising proof-of-principle has been shown for antisense oligonucleotide (AON)-mediated exon skipping as a therapeutic approach for DEB. However, the precise phenotypic effect to be anticipated from exon skipping, and which patient groups could benefit, is not yet clear. To answer these questions, we studied new clinical and molecular data on seven patients from the Dutch EB registry and reviewed the literature on COL7A1 exon skipping variants. We found that phenotypes associated with dominant exon skipping cannot be distinguished from phenotypes caused by other dominant DEB variants. Recessive exon skipping phenotypes are generally relatively mild in the spectrum of recessive DEB. Therefore, for dominant DEB, AON-mediated exon skipping is unlikely to ameliorate the phenotype. In contrast, the overall severity of phenotypes associated with recessive natural exon skipping pivots toward the milder end of the spectrum. Consequently, we anticipate AON-mediated exon skipping for recessive DEB caused by bi-allelic null variants should lead to a clinically relevant improvement of this devastating phenotype.
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Affiliation(s)
- Jeroen Bremer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Elisabeth H van der Heijden
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daryll S Eichhorn
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rowdy Meijer
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcel F Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anna M G Pasmooij
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Peter C Van den Akker
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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10
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Almomani R, Herkert JC, Posafalvi A, Post JG, Boven LG, van der Zwaag PA, Willems PHGM, van Veen-Hof IH, Verhagen JMA, Wessels MW, Nikkels PGJ, Wintjes LT, van den Berg MP, Sinke RJ, Rodenburg RJ, Niezen-Koning KE, van Tintelen JP, Jongbloed JDH. Homozygous damaging SOD2 variant causes lethal neonatal dilated cardiomyopathy. J Med Genet 2019; 57:23-30. [PMID: 31494578 DOI: 10.1136/jmedgenet-2019-106330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND Idiopathic dilated cardiomyopathy (DCM) is recognised to be a heritable disorder, yet clinical genetic testing does not produce a diagnosis in >50% of paediatric patients. Identifying a genetic cause is crucial because this knowledge can affect management options, cardiac surveillance in relatives and reproductive decision-making. In this study, we sought to identify the underlying genetic defect in a patient born to consanguineous parents with rapidly progressive DCM that led to death in early infancy. METHODS AND RESULTS Exome sequencing revealed a potentially pathogenic, homozygous missense variant, c.542G>T, p.(Gly181Val), in SOD2. This gene encodes superoxide dismutase 2 (SOD2) or manganese-superoxide dismutase, a mitochondrial matrix protein that scavenges oxygen radicals produced by oxidation-reduction and electron transport reactions occurring in mitochondria via conversion of superoxide anion (O2 -·) into H2O2. Measurement of hydroethidine oxidation showed a significant increase in O2 -· levels in the patient's skin fibroblasts, as compared with controls, and this was paralleled by reduced catalytic activity of SOD2 in patient fibroblasts and muscle. Lentiviral complementation experiments demonstrated that mitochondrial SOD2 activity could be completely restored on transduction with wild type SOD2. CONCLUSION Our results provide evidence that defective SOD2 may lead to toxic increases in the levels of damaging oxygen radicals in the neonatal heart, which can result in rapidly developing heart failure and death. We propose SOD2 as a novel nuclear-encoded mitochondrial protein involved in severe human neonatal cardiomyopathy, thus expanding the wide range of genetic factors involved in paediatric cardiomyopathies.
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Affiliation(s)
- Rowida Almomani
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Johanna C Herkert
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anna Posafalvi
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan G Post
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ludolf G Boven
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Paul A van der Zwaag
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter H G M Willems
- Department of Biochemistry, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingrid H van Veen-Hof
- Laboratory of Metabolic Diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Liesbeth T Wintjes
- Department of Paediatrics, Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maarten P van den Berg
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Rodenburg
- Department of Paediatrics, Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Klary E Niezen-Koning
- Laboratory of Metabolic Diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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11
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Fokkema IFAC, van der Velde KJ, Slofstra MK, Ruivenkamp CAL, Vogel MJ, Pfundt R, Blok MJ, Lekanne Deprez RH, Waisfisz Q, Abbott KM, Sinke RJ, Rahman R, Nijman IJ, de Koning B, Thijs G, Wieskamp N, Moritz RJG, Charbon B, Saris JJ, den Dunnen JT, Laros JFJ, Swertz MA, van Gijn ME. Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data. Hum Mutat 2019; 40:2230-2238. [PMID: 31433103 PMCID: PMC6900155 DOI: 10.1002/humu.23896] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 02/20/2019] [Revised: 08/05/2019] [Accepted: 08/14/2019] [Indexed: 11/06/2022]
Abstract
Each year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next-generation sequencing (NGS). This requires pathogenicity classification of millions of DNA variants on the standard 5-tier scale. To reduce time spent on data interpretation and increase data quality and reliability, the nine Dutch labs decided to publicly share their classifications. Variant classifications of nearly 100,000 unique variants were catalogued and compared in a centralized MOLGENIS database. Variants classified by more than one center were labeled as "consensus" when classifications agreed, and shared internationally with LOVD and ClinVar. When classifications opposed (LB/B vs. LP/P), they were labeled "conflicting", while other nonconsensus observations were labeled "no consensus". We assessed our classifications using the InterVar software to compare to ACMG 2015 guidelines, showing 99.7% overall consistency with only 0.3% discrepancies. Differences in classifications between Dutch labs or between Dutch labs and ACMG were mainly present in genes with low penetrance or for late onset disorders and highlight limitations of the current 5-tier classification system. The data sharing boosted the quality of DNA diagnostics in Dutch labs, an initiative we hope will be followed internationally. Recently, a positive match with a case from outside our consortium resulted in a more definite disease diagnosis.
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Affiliation(s)
- Ivo F A C Fokkema
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kasper J van der Velde
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Mariska K Slofstra
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Academic Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rubayte Rahman
- Department of Research IT, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Isaäc J Nijman
- Medicine Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gert Thijs
- DGG-Genomics Software Solutions, Agilent Technologies, Leuven, Belgium
| | - Nienke Wieskamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ruben J G Moritz
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart Charbon
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Medicine Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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12
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Yenamandra VK, van den Akker PC, Lemmink HH, Jan SZ, Diercks GFH, Vermeer M, van den Berg MP, van der Meer P, Pasmooij AMG, Sinke RJ, Jonkman MF, Bolling MC. Cardiomyopathy in patients with epidermolysis bullosa simplex with mutations in KLHL24. Br J Dermatol 2018; 179:1181-1183. [PMID: 29779254 DOI: 10.1111/bjd.16797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- V K Yenamandra
- Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands
| | | | - H H Lemmink
- Department of Genetics, Groningen, The Netherlands
| | - S Z Jan
- Department of Genetics, Groningen, The Netherlands
| | | | - M Vermeer
- Department of Cardiology, Groningen, The Netherlands
| | | | | | - A M G Pasmooij
- Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands
| | - R J Sinke
- Department of Genetics, Groningen, The Netherlands
| | - M F Jonkman
- Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands
| | - M C Bolling
- Department of Dermatology, Center for Blistering Diseases, Groningen, The Netherlands
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13
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Alimohamed MZ, Johansson LF, de Boer EN, Splinter E, Klous P, Yilmaz M, Bosga A, van Min M, Mulder AB, Vellenga E, Sinke RJ, Sijmons RH, van den Berg E, Sikkema-Raddatz B. Genetic Screening Test to Detect Translocations in Acute Leukemias by Use of Targeted Locus Amplification. Clin Chem 2018; 64:1096-1103. [DOI: 10.1373/clinchem.2017.286047] [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: 12/19/2017] [Accepted: 04/16/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Over 500 translocations have been identified in acute leukemia. To detect them, most diagnostic laboratories use karyotyping, fluorescent in situ hybridization, and reverse transcription PCR. Targeted locus amplification (TLA), a technique using next-generation sequencing, now allows detection of the translocation partner of a specific gene, regardless of its chromosomal origin. We present a TLA multiplex assay as a potential first-tier screening test for detecting translocations in leukemia diagnostics.
METHODS
The panel includes 17 genes involved in many translocations present in acute leukemias. Procedures were optimized by using a training set of cell line dilutions and 17 leukemia patient bone marrow samples and validated by using a test set of cell line dilutions and a further 19 patient bone marrow samples. Per gene, we determined if its region was involved in a translocation and, if so, the translocation partner. To balance sensitivity and specificity, we introduced a gray zone showing indeterminate translocation calls needing confirmation. We benchmarked our method against results from the 3 standard diagnostic tests.
RESULTS
In patient samples passing QC, we achieved a concordance with benchmarking tests of 81% in the training set and 100% in the test set, after confirmation of 4 and nullification of 3 gray zone calls (in total). In cell line dilutions, we detected translocations in 10% aberrant cells at several genetic loci.
CONCLUSIONS
Multiplex TLA shows promising results as an acute leukemia screening test. It can detect cryptic and other translocations in selected genes. Further optimization may make this assay suitable for diagnostic use.
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Affiliation(s)
- Mohamed Z Alimohamed
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lennart F Johansson
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Eddy N de Boer
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | | | | | | | - Anneke Bosga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | | | - André B Mulder
- University of Groningen, University Medical Center Groningen, Department of Laboratory Medicine, the Netherlands
| | - Edo Vellenga
- University of Groningen, University Medical Center Groningen, Department of Hematology, the Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rolf H Sijmons
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Eva van den Berg
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
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14
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Oldoni F, van Capelleveen JC, Dalila N, Wolters JC, Heeren J, Sinke RJ, Hui DY, Dallinga-Thie GM, Frikke-Schmidt R, Hovingh KG, van de Sluis B, Tybjærg-Hansen A, Kuivenhoven JA. Naturally Occurring Variants in LRP1 (Low-Density Lipoprotein Receptor-Related Protein 1) Affect HDL (High-Density Lipoprotein) Metabolism Through ABCA1 (ATP-Binding Cassette A1) and SR-B1 (Scavenger Receptor Class B Type 1) in Humans. Arterioscler Thromb Vasc Biol 2018; 38:1440-1453. [PMID: 29853565 PMCID: PMC6023722 DOI: 10.1161/atvbaha.117.310309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 09/25/2017] [Accepted: 05/07/2018] [Indexed: 12/14/2022]
Abstract
Supplemental Digital Content is available in the text. Objective— Studies into the role of LRP1 (low-density lipoprotein receptor–related protein 1) in human lipid metabolism are scarce. Although it is known that a common variant in LRP1 (rs116133520) is significantly associated with HDL-C (high-density lipoprotein cholesterol), the mechanism underlying this observation is unclear. In this study, we set out to study the functional effects of 2 rare LRP1 variants identified in subjects with extremely low HDL-C levels. Approach and Results— In 2 subjects with HDL-C below the first percentile for age and sex and moderately elevated triglycerides, we identified 2 rare variants in LRP1: p.Val3244Ile and p.Glu3983Asp. Both variants decrease LRP1 expression and stability. We show in a series of translational experiments that these variants culminate in reduced trafficking of ABCA1 (ATP-binding cassette A1) to the cell membrane. This is accompanied by an increase in cell surface expression of SR-B1 (scavenger receptor class B type 1). Combined these effects may contribute to low HDL-C levels in our study subjects. Supporting these findings, we provide epidemiological evidence that rs116133520 is associated with apo (apolipoprotein) A1 but not with apoB levels. Conclusions— This study provides the first evidence that rare variants in LRP1 are associated with changes in human lipid metabolism. Specifically, this study shows that LRP1 may affect HDL metabolism by virtue of its effect on both ABCA1 and SR-B1.
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Affiliation(s)
- Federico Oldoni
- From the Department of Pediatrics, Section of Molecular Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands (F.O., J.C.W., B.v.d.S., J.A.K.)
| | | | - Nawar Dalila
- Department of Clinical Biochemistry, Rigshospitalet (N.D., R.F.-S., A.T.-H.)
| | - Justina C Wolters
- From the Department of Pediatrics, Section of Molecular Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands (F.O., J.C.W., B.v.d.S., J.A.K.)
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Germany (J.H.)
| | - Richard J Sinke
- Department of Genetics, University Medical Centre Groningen, The Netherlands (R.J.S.)
| | - David Y Hui
- Department of Pathology and Laboratory Medicine, Metabolic Diseases Institute, University of Cincinnati College of Medicine, OH (D.Y.H.)
| | - Geesje M Dallinga-Thie
- Department of Vascular Medicine (J.C.v.C., G.M.D.-T., K.G.H.).,Department Experimental Vascular Medicine (G.M.D.-T.), Academic Medical Center, Amsterdam, The Netherlands
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet (N.D., R.F.-S., A.T.-H.)
| | - Kees G Hovingh
- Department of Vascular Medicine (J.C.v.C., G.M.D.-T., K.G.H.)
| | - Bart van de Sluis
- From the Department of Pediatrics, Section of Molecular Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands (F.O., J.C.W., B.v.d.S., J.A.K.)
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet (N.D., R.F.-S., A.T.-H.).,Copenhagen City Heart Study, Frederiksberg Hospital (A.T.-H.), Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jan Albert Kuivenhoven
- From the Department of Pediatrics, Section of Molecular Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands (F.O., J.C.W., B.v.d.S., J.A.K.)
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15
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Herkert JC, Abbott KM, Birnie E, Meems-Veldhuis MT, Boven LG, Benjamins M, du Marchie Sarvaas GJ, Barge-Schaapveld DQCM, van Tintelen JP, van der Zwaag PA, Vos YJ, Sinke RJ, van den Berg MP, van Langen IM, Jongbloed JDH. Toward an effective exome-based genetic testing strategy in pediatric dilated cardiomyopathy. Genet Med 2018. [DOI: 10.1038/gim.2018.9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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16
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Nibbeling EAR, Duarri A, Verschuuren-Bemelmans CC, Fokkens MR, Karjalainen JM, Smeets CJLM, de Boer-Bergsma JJ, van der Vries G, Dooijes D, Bampi GB, van Diemen C, Brunt E, Ippel E, Kremer B, Vlak M, Adir N, Wijmenga C, van de Warrenburg BPC, Franke L, Sinke RJ, Verbeek DS. Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia. Brain 2017; 140:2860-2878. [PMID: 29053796 DOI: 10.1093/brain/awx251] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 03/20/2017] [Accepted: 08/05/2017] [Indexed: 12/17/2022] Open
Abstract
The autosomal dominant cerebellar ataxias, referred to as spinocerebellar ataxias in genetic nomenclature, are a rare group of progressive neurodegenerative disorders characterized by loss of balance and coordination. Despite the identification of numerous disease genes, a substantial number of cases still remain without a genetic diagnosis. Here, we report five novel spinocerebellar ataxia genes, FAT2, PLD3, KIF26B, EP300, and FAT1, identified through a combination of exome sequencing in genetically undiagnosed families and targeted resequencing of exome candidates in a cohort of singletons. We validated almost all genes genetically, assessed damaging effects of the gene variants in cell models and further consolidated a role for several of these genes in the aetiology of spinocerebellar ataxia through network analysis. Our work links spinocerebellar ataxia to alterations in synaptic transmission and transcription regulation, and identifies these as the main shared mechanisms underlying the genetically diverse spinocerebellar ataxia types.
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Affiliation(s)
- Esther A R Nibbeling
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anna Duarri
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Michiel R Fokkens
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Juha M Karjalainen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cleo J L M Smeets
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jelkje J de Boer-Bergsma
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerben van der Vries
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dennis Dooijes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Giovana B Bampi
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cleo van Diemen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ewout Brunt
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elly Ippel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Berry Kremer
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Monique Vlak
- Department of Neurology, Medical Center Haaglanden and Bronovo-Nebo, Den Hague, The Netherlands
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Israel
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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17
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Turcan I, Pasmooij AM, Gostyński A, van den Akker PC, Lemmink HH, Diercks GF, Pas HH, Sinke RJ, Jonkman MF. Epidermolysis Bullosa Simplex Caused by Distal Truncation of BPAG1-e: An Intermediate Generalized Phenotype with Prurigo Papules. J Invest Dermatol 2017; 137:2227-2230. [DOI: 10.1016/j.jid.2017.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/27/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
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18
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van Diemen CC, Kerstjens-Frederikse WS, Bergman KA, de Koning TJ, Sikkema-Raddatz B, van der Velde JK, Abbott KM, Herkert JC, Löhner K, Rump P, Meems-Veldhuis MT, Neerincx PBT, Jongbloed JDH, van Ravenswaaij-Arts CM, Swertz MA, Sinke RJ, van Langen IM, Wijmenga C. Rapid Targeted Genomics in Critically Ill Newborns. Pediatrics 2017; 140:peds.2016-2854. [PMID: 28939701 DOI: 10.1542/peds.2016-2854] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/10/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/or invasive diagnostic testing. A previous retrospective study in a research setting showed promising results with diagnoses in 57%, but patients were highly selected for known and likely Mendelian disorders. The aim of our prospective study was to assess the speed and yield of rapid targeted genomic diagnostics for clinical application. METHODS We included 23 critically ill children younger than 12 months in ICUs over a period of 2 years. A quick diagnosis could not be made after routine clinical evaluation and diagnostics. Targeted analysis of 3426 known disease genes was performed by using whole-genome sequencing data. We measured diagnostic yield, turnaround times, and clinical consequences. RESULTS A genetic diagnosis was obtained in 7 patients (30%), with a median turnaround time of 12 days (ranging from 5 to 23 days). We identified compound heterozygous mutations in the EPG5 gene (Vici syndrome), the RMND1 gene (combined oxidative phosphorylation deficiency-11), and the EIF2B5 gene (vanishing white matter), and homozygous mutations in the KLHL41 gene (nemaline myopathy), the GFER gene (progressive mitochondrial myopathy), and the GLB1 gene (GM1-gangliosidosis). In addition, a 1p36.33p36.32 microdeletion was detected in a child with cardiomyopathy. CONCLUSIONS Rapid targeted genomics combined with copy number variant detection adds important value in the neonatal and pediatric intensive care setting. It led to a fast diagnosis in 30% of critically ill children for whom the routine clinical workup was unsuccessful.
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Affiliation(s)
| | | | - Klasien A Bergman
- Beatrix Children's Hospital, University Medical Center Groningen, Groningen, Netherlands
| | - Tom J de Koning
- Department of Genetics, University of Groningen; and.,Beatrix Children's Hospital, University Medical Center Groningen, Groningen, Netherlands
| | | | | | | | | | | | - Patrick Rump
- Department of Genetics, University of Groningen; and
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19
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Miyake N, Wolf NI, Cayami FK, Crawford J, Bley A, Bulas D, Conant A, Bent SJ, Gripp KW, Hahn A, Humphray S, Kimura-Ohba S, Kingsbury Z, Lajoie BR, Lal D, Micha D, Pizzino A, Sinke RJ, Sival D, Stolte-Dijkstra I, Superti-Furga A, Ulrick N, Taft RJ, Ogata T, Ozono K, Matsumoto N, Neubauer BA, Simons C, Vanderver A. X-linked hypomyelination with spondylometaphyseal dysplasia (H-SMD) associated with mutations in AIFM1. Neurogenetics 2017; 18:185-194. [PMID: 28842795 PMCID: PMC5705759 DOI: 10.1007/s10048-017-0520-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/04/2017] [Indexed: 01/12/2023]
Abstract
An X-linked condition characterized by the combination of hypomyelinating leukodystrophy and spondylometaphyseal dysplasia (H-SMD) has been observed in only four families, with linkage to Xq25-27, and recent genetic characterization in two families with a common AIFM1 mutation. In our study, 12 patients (6 families) with H-SMD were identified and underwent comprehensive assessment accompanied by whole-exome sequencing (WES). Pedigree analysis in all families was consistent with X-linked recessive inheritance. Presentation typically occurred between 12 and 36 months. In addition to the two disease-defining features of spondylometaphyseal dysplasia and hypomyelination on MRI, common clinical signs and symptoms included motor deterioration, spasticity, tremor, ataxia, dysarthria, cognitive defects, pulmonary hypertension, nystagmus, and vision loss due to retinopathy. The course of the disease was slowly progressive. All patients had maternally inherited or de novo mutations in or near exon 7 of AIFM1, within a region of 70 bp, including synonymous and intronic changes. AIFM1 mutations have previously been associated with neurologic presentations as varied as intellectual disability, hearing loss, neuropathy, and striatal necrosis, while AIFM1 mutations in this small region present with a distinct phenotype implicating bone. Analysis of cell lines derived from four patients identified significant reductions in AIFM1 mRNA and protein levels in osteoblasts. We hypothesize that AIFM1 functions in bone metabolism and myelination and is responsible for the unique phenotype in this condition.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nicole I Wolf
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
| | - Ferdy K Cayami
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Annette Bley
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Dorothy Bulas
- Department of Diagnostic Imaging and Radiology, Children's National Medical Center, Washington, DC, USA
| | - Alex Conant
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Stephen J Bent
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Andreas Hahn
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Sean Humphray
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | - Shihoko Kimura-Ohba
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Zoya Kingsbury
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | | | - Dennis Lal
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, USA
| | - Dimitra Micha
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Amy Pizzino
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Deborah Sival
- Department of Child Neurology, University Hospital Groningen, Groningen, Netherlands
| | - Irene Stolte-Dijkstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Nicole Ulrick
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Illumina, Inc, San Diego, CA, USA.,George Washington University School of Medicine, Washington, DC, USA
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Bernd A Neubauer
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Adeline Vanderver
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA.,Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland.,Children's Hospital of Philadelphia, Philadelphia, PA, USA
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20
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Turcan I, Pasmooij AMG, Van den Akker PC, Lemmink H, Sinke RJ, Jonkman MF. Association of Epidermolysis Bullosa Simplex With Mottled Pigmentation and EXPH5 Mutations. JAMA Dermatol 2017; 152:1137-1141. [PMID: 27384765 DOI: 10.1001/jamadermatol.2016.2268] [Citation(s) in RCA: 16] [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: 11/14/2022]
Abstract
Importance Epidermolysis bullosa simplex (EBS) is a group of clinically and genetically diverse mechanobullous genodermatoses characterized by the fragility of skin and mucous membranes. Recently, mutations in EXPH5 encoding exophilin-5 (also known as Slac2-b, an effector protein involved in intracellular vesicle trafficking and exosome secretion) have been implicated in the pathophysiology of EBS. Herein, we report a novel homozygous nonsense mutation in EXPH5 responsible for an EBS subtype with mottled pigmentation. Objective To identify the gene mutation(s) accountable for the mottled pigmentation phenotype in a patient with suspected inherited skin fragility disorder. Design, Setting, and Participant Data for this case report were acquired in an outpatient clinic and concern a referral from the primary care physician to the national Center for Blistering Diseases in The Netherlands. Data were acquired and analyzed from 2014 to 2016. Main Outcomes and Measures Clinical examination and investigation were performed of the molecular basis of patient's skin fragility and mottled pigmentation phenotype. Electron microscopy studies described the underlying abnormalities on an ultrastructural level. Results The clinical phenotype is characterized by mild generalized skin fragility, trauma-induced skin blistering since infancy, and development of remarkable diffuse mottled pigmentation on the trunk and proximal extremities. Sequencing the complete set of genes associated with epidermolysis bullosa revealed a homozygous nonsense mutation in exon 6 of EXPH5: c.3917C>G, p.Ser1306*. Electron microscopy revealed disruption of keratin filament cytoskeleton and accumulation of melanosomes in a disordered distribution in the keratinocytes. Conclusions and Relevance To our knowledge, the current study illustrates the first clinically well-documented, mottled pigmentation phenotype related to a novel EXPH5 mutation. In addition, by means of electron microscopy image analysis, it proposes a hypothesis for the pigmentary changes in this rare autosomal recessive EBS subtype. These findings expand the genetic and phenotypic spectrum of human inherited skin fragility disorders, and we propose the addition of EBS resulting from EXPH5 mutations to the EBS-mottled pigmentation subtype.
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Affiliation(s)
- Iana Turcan
- Center for Blistering Diseases, Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anna M G Pasmooij
- Center for Blistering Diseases, Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Peter C Van den Akker
- Center for Blistering Diseases, Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands2Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marcel F Jonkman
- Center for Blistering Diseases, Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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21
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van Egmond ME, Lugtenberg CHA, Brouwer OF, Contarino MF, Fung VSC, Heiner-Fokkema MR, van Hilten JJ, van der Hout AH, Peall KJ, Sinke RJ, Roze E, Verschuuren-Bemelmans CC, Willemsen MA, Wolf NI, Tijssen MA, de Koning TJ. A post hoc study on gene panel analysis for the diagnosis of dystonia. Mov Disord 2017; 32:569-575. [PMID: 28186668 DOI: 10.1002/mds.26937] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/21/2016] [Accepted: 01/08/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genetic disorders causing dystonia show great heterogeneity. Recent studies have suggested that next-generation sequencing techniques such as gene panel analysis can be effective in diagnosing heterogeneous conditions. The objective of this study was to investigate whether dystonia patients with a suspected genetic cause could benefit from the use of gene panel analysis. METHODS In this post hoc study, we describe gene panel analysis results of 61 dystonia patients (mean age, 31 years; 72% young onset) in our tertiary referral center. The panel covered 94 dystonia-associated genes. As comparison with a historic cohort was not possible because of the rapidly growing list of dystonia genes, we compared the diagnostic workup with and without gene panel analysis in the same patients. The workup without gene panel analysis (control group) included theoretical diagnostic strategies formulated by independent experts in the field, based on detailed case descriptions. The primary outcome measure was diagnostic yield; secondary measures were cost and duration of diagnostic workup. RESULTS Workup with gene panel analysis led to a confirmed molecular diagnosis in 14.8%, versus 7.4% in the control group (P = 0.096). In the control group, on average 3 genes/case were requested. The mean costs were lower in the gene panel analysis group (€1822/case) than in the controls (€2660/case). The duration of the workup was considerably shorter with gene panel analysis (28 vs 102 days). CONCLUSIONS Gene panel analysis facilitates molecular diagnosis in complex cases of dystonia, with a good diagnostic yield (14.8%), a quicker diagnostic workup, and lower costs, representing a major improvement for patients and their families. © 2016 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Martje E van Egmond
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands.,Ommelander Ziekenhuis Groningen, Department of Neurology, Delfzijl and Winschoten, the Netherlands
| | - Coen H A Lugtenberg
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Oebele F Brouwer
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Maria Fiorella Contarino
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Neurology, Haga Teaching Hospital, The Hague, the Netherlands
| | - Victor S C Fung
- Movement Disorders Unit, Department of Neurology, Westmead Hospital & Sydney Medical School, University of Sydney, Sydney, Australia
| | - M Rebecca Heiner-Fokkema
- University of Groningen, University Medical Centre Groningen, Department of Laboratory Medicine, Groningen, the Netherlands
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Annemarie H van der Hout
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Kathryn J Peall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Richard J Sinke
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Emmanuel Roze
- Département de Neurologie, AP-HP, Hôpital Pitié-Salpêtrière and Sorbonne Universités, Université Pierre and Marie Curie, Institut du Cerveau et de la Moelle épinière, Paris, France
| | | | - Michel A Willemsen
- Radboud University Medical Centre, Department of Paediatric Neurology, Nijmegen, the Netherlands
| | - Nicole I Wolf
- VU University Medical Centre, Department of Child Neurology and Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Marina A Tijssen
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Tom J de Koning
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands.,University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Centre Groningen, Department of Paediatrics, Groningen, the Netherlands
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22
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Nibbeling EAR, Delnooz CCS, de Koning TJ, Sinke RJ, Jinnah HA, Tijssen MAJ, Verbeek DS. Using the shared genetics of dystonia and ataxia to unravel their pathogenesis. Neurosci Biobehav Rev 2017; 75:22-39. [PMID: 28143763 DOI: 10.1016/j.neubiorev.2017.01.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 07/07/2016] [Revised: 12/09/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022]
Abstract
In this review we explore the similarities between spinocerebellar ataxias and dystonias, and suggest potentially shared molecular pathways using a gene co-expression network approach. The spinocerebellar ataxias are a group of neurodegenerative disorders characterized by coordination problems caused mainly by atrophy of the cerebellum. The dystonias are another group of neurological movement disorders linked to basal ganglia dysfunction, although evidence is now pointing to cerebellar involvement as well. Our gene co-expression network approach identified 99 shared genes and showed the involvement of two major pathways: synaptic transmission and neurodevelopment. These pathways overlapped in the two disorders, with a large role for GABAergic signaling in both. The overlapping pathways may provide novel targets for disease therapies. We need to prioritize variants obtained by whole exome sequencing in the genes associated with these pathways in the search for new pathogenic variants, which can than be used to help in the genetic counseling of patients and their families.
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Affiliation(s)
- Esther A R Nibbeling
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cathérine C S Delnooz
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Hyder A Jinnah
- Departments of Neurology, Human Genetics and Pediatrics, Emory Clinic, Atlanta, USA
| | - Marina A J Tijssen
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Dineke S Verbeek
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
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23
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van der Velde KJ, de Boer EN, van Diemen CC, Sikkema-Raddatz B, Abbott KM, Knopperts A, Franke L, Sijmons RH, de Koning TJ, Wijmenga C, Sinke RJ, Swertz MA. GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biol 2017; 18:6. [PMID: 28093075 PMCID: PMC5240400 DOI: 10.1186/s13059-016-1141-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 07/13/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023] Open
Abstract
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes. In a benchmark on 18 clinical gene sets, we achieve a sensitivity of 91.4% and a specificity of 76.9%. This accuracy is unmatched by 12 other tools. We provide GAVIN as an online MOLGENIS service to annotate VCF files and as an open source executable for use in bioinformatic pipelines. It can be found at http://molgenis.org/gavin.
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Affiliation(s)
- K Joeri van der Velde
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eddy N de Boer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alain Knopperts
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tom J de Koning
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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24
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Plantinga M, Birnie E, Abbott KM, Sinke RJ, Lucassen AM, Schuurmans J, Kaplan S, Verkerk MA, Ranchor AV, van Langen IM. Population-based preconception carrier screening: how potential users from the general population view a test for 50 serious diseases. Eur J Hum Genet 2016; 24:1417-23. [PMID: 27165008 PMCID: PMC5027688 DOI: 10.1038/ejhg.2016.43] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 10/29/2015] [Revised: 02/17/2016] [Accepted: 04/07/2016] [Indexed: 11/09/2022] Open
Abstract
With the increased international focus on personalized health care and preventive medicine, next-generation sequencing (NGS) has substantially expanded the options for carrier screening of serious, recessively inherited diseases. NGS screening tests not only offer reproductive options not previously available to couples, but they may also ultimately reduce the number of children born with devastating disorders. To date, preconception carrier screening (PCS) has largely targeted single diseases such as cystic fibrosis, but NGS allows the testing of many genes or diseases simultaneously. We have developed an expanded NGS PCS test for couples; simultaneously it covers 50 very serious, early-onset, autosomal recessive diseases that are untreatable. This is the first, noncommercial, population-based, expanded PCS test to be offered prospectively to couples in a health-care setting in Europe. So far, little is known about how potential users view such a PCS test. We therefore performed an online survey in 2014 among 500 people from the target population in the Netherlands. We enquired about their intention to take an expanded PCS test if one was offered, and through which provider they would like to see it offered. One-third of the respondents said they would take such a test were it to be offered. The majority (44%) preferred the test to be offered via their general practitioner (GP) and 58% would be willing to pay for the test, with a median cost of [euro ]75. Our next step is to perform an implementation study in which this PCS test will be provided via selected GPs in the Northern Netherlands.
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Affiliation(s)
- Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Erwin Birnie
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Juliette Schuurmans
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Seyma Kaplan
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian A Verkerk
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Adelita V Ranchor
- Department of Health Psychology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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25
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Smeets CJLM, Zmorzyńska J, Melo MN, Stargardt A, Dooley C, Bakalkin G, McLaughlin J, Sinke RJ, Marrink SJ, Reits E, Verbeek DS. Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23. Hum Mol Genet 2016; 25:2728-2737. [PMID: 27260403 DOI: 10.1093/hmg/ddw130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/31/2016] [Accepted: 04/24/2016] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 23 (SCA23) is caused by missense mutations in prodynorphin, encoding the precursor protein for the opioid neuropeptides α-neoendorphin, Dynorphin (Dyn) A and Dyn B, leading to neurotoxic elevated mutant Dyn A levels. Dyn A acts on opioid receptors to reduce pain in the spinal cord, but its cerebellar function remains largely unknown. Increased concentration of or prolonged exposure to Dyn A is neurotoxic and these deleterious effects are very likely caused by an N-methyl-d-aspartate-mediated non-opioid mechanism as Dyn A peptides were shown to bind NMDA receptors and potentiate their glutamate-evoked currents. In the present study, we investigated the cellular mechanisms underlying SCA23-mutant Dyn A neurotoxicity. We show that SCA23 mutations in the Dyn A-coding region disrupted peptide secondary structure leading to a loss of the N-terminal α-helix associated with decreased κ-opioid receptor affinity. Additionally, the altered secondary structure led to increased peptide stability of R6W and R9C Dyn A, as these peptides showed marked degradation resistance, which coincided with decreased peptide solubility. Notably, L5S Dyn A displayed increased degradation and no aggregation. R6W and wt Dyn A peptides were most toxic to primary cerebellar neurons. For R6W Dyn A, this is likely because of a switch from opioid to NMDA- receptor signalling, while for wt Dyn A, this switch was not observed. We propose that the pathology of SCA23 results from converging mechanisms of loss of opioid-mediated neuroprotection and NMDA-mediated excitotoxicity.
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Affiliation(s)
- Cleo J L M Smeets
- Department of Genetics, University of Groningen, University Medical Centre GroningenGroningen, the Netherlands
| | - Justyna Zmorzyńska
- Department of Genetics, University of Groningen, University Medical Centre GroningenGroningen, the Netherlands
| | - Manuel N Melo
- Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Anita Stargardt
- Department of Cell Biology and Histology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Colette Dooley
- Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, USA
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Jay McLaughlin
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Centre GroningenGroningen, the Netherlands
| | - Siewert-Jan Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Eric Reits
- Department of Cell Biology and Histology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University of Groningen, University Medical Centre GroningenGroningen, the Netherlands
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26
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Turcan I, Pasmooij AMG, van den Akker PC, Lemmink H, Halmos GB, Sinke RJ, Jonkman MF. Heterozygosity for a Novel Missense Mutation in theITGB4Gene Associated With Autosomal Dominant Epidermolysis Bullosa. JAMA Dermatol 2016; 152:558-62. [DOI: 10.1001/jamadermatol.2015.5236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Iana Turcan
- Department of Dermatology, Center for Blistering Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands,
| | - Anna M. G. Pasmooij
- Department of Dermatology, Center for Blistering Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands,
| | - Peter C. van den Akker
- Department of Dermatology, Center for Blistering Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands, 2Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Neth
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Gyorgy B. Halmos
- Department of Otorhinolaryngology–Head and Neck Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Richard J. Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marcel F. Jonkman
- Department of Dermatology, Center for Blistering Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands,
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27
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Johansson LF, van Dijk F, de Boer EN, van Dijk-Bos KK, Jongbloed JDH, van der Hout AH, Westers H, Sinke RJ, Swertz MA, Sijmons RH, Sikkema-Raddatz B. CoNVaDING: Single Exon Variation Detection in Targeted NGS Data. Hum Mutat 2016; 37:457-64. [PMID: 26864275 DOI: 10.1002/humu.22969] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [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: 11/26/2015] [Accepted: 01/27/2016] [Indexed: 12/23/2022]
Abstract
We have developed a tool for detecting single exon copy-number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control (QC) metric, that excludes or flags low-quality exons. Since this QC shows exactly which exons can be reliably analyzed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high-quality targets in 320 samples analyzed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions.
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Affiliation(s)
- Lennart F Johansson
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Freerk van Dijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Eddy N de Boer
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Krista K van Dijk-Bos
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Jan D H Jongbloed
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Annemieke H van der Hout
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Helga Westers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Rolf H Sijmons
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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28
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Rump P, Jazayeri O, van Dijk-Bos KK, Johansson LF, van Essen AJ, Verheij JBGM, Veenstra-Knol HE, Redeker EJW, Mannens MMAM, Swertz MA, Alizadeh BZ, van Ravenswaaij-Arts CMA, Sinke RJ, Sikkema-Raddatz B. Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly. BMC Med Genomics 2016; 9:7. [PMID: 26846091 PMCID: PMC4743197 DOI: 10.1186/s12920-016-0167-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background Clinical and genetic heterogeneity in monogenetic disorders represents a major diagnostic challenge. Although the presence of particular clinical features may aid in identifying a specific cause in some cases, the majority of patients remain undiagnosed. Here, we investigated the utility of whole-exome sequencing as a diagnostic approach for establishing a molecular diagnosis in a highly heterogeneous group of patients with varied intellectual disability and microcephaly. Methods Whole-exome sequencing was performed in 38 patients, including three sib-pairs, in addition to or in parallel with genetic analyses that were performed during the diagnostic work-up of the study participants. Results In ten out of these 35 families (29 %), we found mutations in genes already known to be related to a disorder in which microcephaly is a main feature. Two unrelated patients had mutations in the ASPM gene. In seven other patients we found mutations in RAB3GAP1, RNASEH2B, KIF11, ERCC8, CASK, DYRK1A and BRCA2. In one of the sib-pairs, mutations were found in the RTTN gene. Mutations were present in seven out of our ten families with an established etiological diagnosis with recessive inheritance. Conclusions We demonstrate that whole-exome sequencing is a powerful tool for the diagnostic evaluation of patients with highly heterogeneous neurodevelopmental disorders such as intellectual disability with microcephaly. Our results confirm that autosomal recessive disorders are highly prevalent among patients with microcephaly. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0167-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Rump
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Omid Jazayeri
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Krista K van Dijk-Bos
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Centre Groningen, Genomics Coordination Centre, Groningen, The Netherlands.
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Johanna B G M Verheij
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Egbert J W Redeker
- Department of Clinical Genetics, University of Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands.
| | - Marcel M A M Mannens
- Department of Clinical Genetics, University of Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands.
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Genomics Coordination Centre, Groningen, The Netherlands.
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
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29
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Almomani R, Verhagen JM, Herkert JC, Brosens E, van Spaendonck-Zwarts KY, Asimaki A, van der Zwaag PA, Frohn-Mulder IM, Bertoli-Avella AM, Boven LG, van Slegtenhorst MA, van der Smagt JJ, van IJcken WF, Timmer B, van Stuijvenberg M, Verdijk RM, Saffitz JE, du Plessis FA, Michels M, Hofstra RM, Sinke RJ, van Tintelen JP, Wessels MW, Jongbloed JD, van de Laar IM. Biallelic Truncating Mutations in ALPK3 Cause Severe Pediatric Cardiomyopathy. J Am Coll Cardiol 2016; 67:515-25. [DOI: 10.1016/j.jacc.2015.10.093] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 10/22/2022]
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30
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Jazayeri O, Liu X, van Diemen CC, Bakker-van Waarde WM, Sikkema-Raddatz B, Sinke RJ, Zhang J, van Ravenswaaij-Arts CM. A novel homozygous insertion and review of published mutations in the NNT gene causing familial glucocorticoid deficiency (FGD). Eur J Med Genet 2015; 58:642-9. [DOI: 10.1016/j.ejmg.2015.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/28/2022]
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31
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Widowati T, Melhem S, Patria SY, de Graaf BM, Sinke RJ, Viel M, Dijkhuis J, Sadewa AH, Purwohardjono R, Soenarto Y, Hofstra RM, Sribudiani Y. RET and EDNRB mutation screening in patients with Hirschsprung disease: Functional studies and its implications for genetic counseling. Eur J Hum Genet 2015; 24:823-9. [PMID: 26395553 DOI: 10.1038/ejhg.2015.214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 12/22/2022] Open
Abstract
Hirschsprung disease (HSCR) is a major cause of chronic constipation in children. HSCR can be caused by germline mutations in RET and EDNRB. Defining causality of the mutations identified is difficult and almost exclusively based on in silico predictions. Therefore, the reported frequency of pathogenic mutations might be overestimated. We combined mutation analysis with functional assays to determine the frequencies of proven pathogenic RET and EDNRB mutations in HSCR. We sequenced RET and EDNRB in 57 HSCR patients. The identified RET-coding variants were introduced into RET constructs and these were transfected into HEK293 cells to determine RET phosphorylation and activation via ERK. An exon trap experiment was performed to check a possible splice-site mutation. We identified eight rare RET-coding variants, one possible splice-site variant, but no rare EDNRB variants. Western blotting showed that three coding variants p.(Pr270Leu), p.(Ala756Val) and p.(Tyr1062Cys) resulted in lower activation of RET. Moreover, only two RET variants (p.(Ala756Val) and p.(Tyr1062Cys)) resulted in reduced ERK activation. Splice-site assays on c.1880-11A>G could not confirm its pathogenicity. Our data suggest that indeed almost half of the identified rare variants are proven pathogenic and that, hence, functional studies are essential for proper genetic counseling.
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Affiliation(s)
- Titis Widowati
- Department of Pediatric, Faculty of Medicine, Universitas Gadjah Mada, Prof.Dr Sardjito Hospital, Yogyakarta, Indonesia
| | - Shamiram Melhem
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Suryono Y Patria
- Department of Pediatric, Faculty of Medicine, Universitas Gadjah Mada, Prof.Dr Sardjito Hospital, Yogyakarta, Indonesia
| | - Bianca M de Graaf
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Richard J Sinke
- Department of Genetic, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn Viel
- Department of Genetic, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jos Dijkhuis
- Department of Genetic, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ahmad H Sadewa
- Department of Biochemistry, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rochadi Purwohardjono
- Department of Pediatric Surgery, Faculty of Medicine, Universitas Gadjah Mada, Prof.Dr Sardjito Hospital, Yogyakarta, Indonesia
| | - Yati Soenarto
- Department of Pediatric, Faculty of Medicine, Universitas Gadjah Mada, Prof.Dr Sardjito Hospital, Yogyakarta, Indonesia
| | - Robert Mw Hofstra
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Yunia Sribudiani
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
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32
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van Egmond ME, Kuiper A, Eggink H, Sinke RJ, Brouwer OF, Verschuuren-Bemelmans CC, Sival DA, Tijssen MAJ, de Koning TJ. Dystonia in children and adolescents: a systematic review and a new diagnostic algorithm. J Neurol Neurosurg Psychiatry 2015; 86:774-81. [PMID: 25395479 DOI: 10.1136/jnnp-2014-309106] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/28/2014] [Indexed: 11/03/2022]
Abstract
Early aetiological diagnosis is of paramount importance for childhood dystonia because some of the possible underlying conditions are treatable. Numerous genetic and non-genetic causes have been reported, and diagnostic workup is often challenging, time consuming and costly. Recently, a paradigm shift has occurred in molecular genetic diagnostics, with next-generation sequencing techniques now allowing us to analyse hundreds of genes simultaneously. To ensure that patients benefit from these new techniques, adaptation of current diagnostic strategies is needed. On the basis of a systematic literature review of dystonia with onset in childhood or adolescence, we propose a novel diagnostic strategy with the aim of helping clinicians determine which patients may benefit by applying these new genetic techniques and which patients first require other investigations. We also provide an up-to-date list of candidate genes for a dystonia gene panel, based on a detailed literature search up to 20 October 2014. While new genetic techniques are certainly not a panacea, possible advantages of our proposed strategy include earlier diagnosis and avoidance of unnecessary investigations. It will therefore shorten the time of uncertainty for patients and their families awaiting a definite diagnosis.
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Affiliation(s)
- Martje E van Egmond
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Anouk Kuiper
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Hendriekje Eggink
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Oebele F Brouwer
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | | | - Deborah A Sival
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Marina A J Tijssen
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
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Duarri A, Lin MCA, Fokkens MR, Meijer M, Smeets CJLM, Nibbeling EAR, Boddeke E, Sinke RJ, Kampinga HH, Papazian DM, Verbeek DS. Spinocerebellar ataxia type 19/22 mutations alter heterocomplex Kv4.3 channel function and gating in a dominant manner. Cell Mol Life Sci 2015; 72:3387-99. [PMID: 25854634 PMCID: PMC4531139 DOI: 10.1007/s00018-015-1894-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/05/2015] [Accepted: 03/24/2015] [Indexed: 12/14/2022]
Abstract
The dominantly inherited cerebellar ataxias are a heterogeneous group of neurodegenerative disorders caused by Purkinje cell loss in the cerebellum. Recently, we identified loss-of-function mutations in the KCND3 gene as the cause of spinocerebellar ataxia type 19/22 (SCA19/22), revealing a previously unknown role for the voltage-gated potassium channel, Kv4.3, in Purkinje cell survival. However, how mutant Kv4.3 affects wild-type Kv4.3 channel functioning remains unknown. We provide evidence that SCA19/22-mutant Kv4.3 exerts a dominant negative effect on the trafficking and surface expression of wild-type Kv4.3 in the absence of its regulatory subunit, KChIP2. Notably, this dominant negative effect can be rescued by the presence of KChIP2. We also found that all SCA19/22-mutant subunits either suppress wild-type Kv4.3 current amplitude or alter channel gating in a dominant manner. Our findings suggest that altered Kv4.3 channel localization and/or functioning resulting from SCA19/22 mutations may lead to Purkinje cell loss, neurodegeneration and ataxia.
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Affiliation(s)
- Anna Duarri
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30 001, 9700 RB, Groningen, The Netherlands
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Deelen P, Zhernakova DV, de Haan M, van der Sijde M, Bonder MJ, Karjalainen J, van der Velde KJ, Abbott KM, Fu J, Wijmenga C, Sinke RJ, Swertz MA, Franke L. Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels. Genome Med 2015; 7:30. [PMID: 25954321 PMCID: PMC4423486 DOI: 10.1186/s13073-015-0152-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [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: 11/25/2014] [Accepted: 03/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves. Methods We downloaded the raw reads for all available human RNA-seq datasets. Using these reads we performed gene expression quantification. All samples were jointly normalized and subjected to a strict quality control. We also derived genotypes using the RNA-seq reads and used imputation to infer non-coding variants. This allowed us to perform eQTL mapping and ASE analyses jointly on all samples that passed quality control. Our results were validated using samples for which DNA-seq genotypes were available. Results 4,978 public human RNA-seq runs, representing many different tissues and cell-types, passed quality control. Even though these data originated from many different laboratories, samples reflecting the same cell type clustered together, suggesting that technical biases due to different sequencing protocols are limited. In a joint analysis on the 1,262 samples with high quality genotypes, we identified cis-eQTLs effects for 8,034 unique genes (at a false discovery rate ≤0.05). eQTL mapping on individual tissues revealed that a limited number of samples already suffice to identify tissue-specific eQTLs for known disease-associated genetic variants. Additionally, we observed strong ASE effects for 34 rare pathogenic variants, corroborating previously observed effects on the corresponding protein levels. Conclusions By deriving and imputing genotypes from RNA-seq data, it is possible to identify both eQTLs and ASE effects. Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0152-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands ; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, 9700 RB Groningen, The Netherlands
| | - Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Mark de Haan
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands ; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, 9700 RB Groningen, The Netherlands
| | - Marijke van der Sijde
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Juha Karjalainen
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - K Joeri van der Velde
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands ; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, 9700 RB Groningen, The Netherlands
| | - Kristin M Abbott
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands ; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, 9700 RB Groningen, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
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Duarri A, Nibbeling EAR, Fokkens MR, Meijer M, Boerrigter M, Verschuuren-Bemelmans CC, Kremer BPH, van de Warrenburg BP, Dooijes D, Boddeke E, Sinke RJ, Verbeek DS. Functional analysis helps to define KCNC3 mutational spectrum in Dutch ataxia cases. PLoS One 2015; 10:e0116599. [PMID: 25756792 PMCID: PMC4355074 DOI: 10.1371/journal.pone.0116599] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 09/16/2014] [Accepted: 12/12/2014] [Indexed: 12/03/2022] Open
Abstract
Spinocerebellar ataxia type 13 (SCA13) is an autosomal dominantly inherited neurodegenerative disorder of the cerebellum caused by mutations in the voltage gated potassium channel KCNC3. To identify novel pathogenic SCA13 mutations in KCNC3 and to gain insights into the disease prevalence in the Netherlands, we sequenced the entire coding region of KCNC3 in 848 Dutch cerebellar ataxia patients with familial or sporadic origin. We evaluated the pathogenicity of the identified variants by co-segregation analysis and in silico prediction followed by biochemical and electrophysiological studies. We identified 19 variants in KCNC3 including 2 non-coding, 11 missense and 6 synonymous variants. Two missense variants did not co-segregate with the disease and were excluded as potentially disease-causing mutations. We also identified the previously reported p.R420H and p.R423H mutations in our cohort. Of the remaining 7 missense variants, functional analysis revealed that 2 missense variants shifted Kv3.3 channel activation to more negative voltages. These variations were associated with early disease onset and mild intellectual disability. Additionally, one other missense variant shifted channel activation to more positive voltages and was associated with spastic ataxic gait. Whereas, the remaining missense variants did not change any of the channel characteristics. Of these three functional variants, only one variant was in silico predicted to be damaging and segregated with disease. The other two variants were in silico predicted to be benign and co-segregation analysis was not optimal or could only be partially confirmed. Therefore, we conclude that we have identified at least one novel pathogenic mutation in KCNC3 that cause SCA13 and two additionally potential SCA13 mutations. This leads to an estimate of SCA13 prevalence in the Netherlands to be between 0.6% and 1.3%.
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Affiliation(s)
- Anna Duarri
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Esther A. R. Nibbeling
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel R. Fokkens
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Michel Meijer
- Department of Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melissa Boerrigter
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Berry P. H. Kremer
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Dennis Dooijes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik Boddeke
- Department of Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J. Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dineke S. Verbeek
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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de Koning TJ, Jongbloed JDH, Sikkema-Raddatz B, Sinke RJ. Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: the opportunities and challenges. Expert Rev Mol Diagn 2014; 15:61-70. [PMID: 25367078 DOI: 10.1586/14737159.2015.976555] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.
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Affiliation(s)
- Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, CB 50, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Affiliation(s)
- Federico Oldoni
- From the Departments of Molecular Genetics (F.O., J.A.K.) and Genetics (R.J.S.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Richard J. Sinke
- From the Departments of Molecular Genetics (F.O., J.A.K.) and Genetics (R.J.S.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jan Albert Kuivenhoven
- From the Departments of Molecular Genetics (F.O., J.A.K.) and Genetics (R.J.S.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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van Egmond ME, Verschuuren-Bemelmans CC, Nibbeling EA, Elting JWJ, Sival DA, Brouwer OF, de Vries JJ, Kremer HP, Sinke RJ, Tijssen MA, de Koning TJ. Ramsay hunt syndrome: Clinical characterization of progressive myoclonus ataxia caused by GOSR2
mutation. Mov Disord 2013; 29:139-43. [DOI: 10.1002/mds.25704] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 07/18/2013] [Accepted: 09/11/2013] [Indexed: 11/09/2022] Open
Affiliation(s)
- Martje E. van Egmond
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | | | - Esther A. Nibbeling
- Department of Genetics; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Jan Willem J. Elting
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Deborah A. Sival
- Department of Pediatrics; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Oebele F. Brouwer
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Jeroen J. de Vries
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Hubertus P. Kremer
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Richard J. Sinke
- Department of Genetics; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Marina A. Tijssen
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
| | - Tom J. de Koning
- Department of Neurology; University of Groningen, University Medical Center Groningen; The Netherlands
- Department of Genetics; University of Groningen, University Medical Center Groningen; The Netherlands
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Stalpers XL, Verrips A, Poll-The BT, Cobben JM, Snoeck IN, de Coo IF, Brooks A, Bulk S, Gooskens R, Fock A, Verschuuren-Bemelmans C, Sinke RJ, de Visser M, Lemmink HH. Clinical and mutational characteristics of spinal muscular atrophy with respiratory distress type 1 in the Netherlands. Neuromuscul Disord 2013; 23:461-8. [DOI: 10.1016/j.nmd.2013.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 10/27/2022]
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Sikkema-Raddatz B, Johansson LF, de Boer EN, Almomani R, Boven LG, van den Berg MP, van Spaendonck-Zwarts KY, van Tintelen JP, Sijmons RH, Jongbloed JDH, Sinke RJ. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat 2013; 34:1035-42. [PMID: 23568810 DOI: 10.1002/humu.22332] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/02/2013] [Indexed: 11/12/2022]
Abstract
Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next-generation sequencing (NGS), in which a selected fraction of genes is sequenced, may circumvent these shortcomings. We aimed to determine whether the sensitivity and specificity of targeted NGS is equal to those of SS. We constructed a targeted enrichment kit that includes 48 genes associated with hereditary cardiomyopathies. In total, 84 individuals with cardiomyopathies were sequenced using 151 bp paired-end reads on an Illumina MiSeq sequencer. The reproducibility was tested by repeating the entire procedure for five patients. The coverage of ≥30 reads per nucleotide, our major quality criterion, was 99% and in total ∼21,000 variants were identified. Confirmation with SS was performed for 168 variants (155 substitutions, 13 indels). All were confirmed, including a deletion of 18 bp and an insertion of 6 bp. The reproducibility was nearly 100%. We demonstrate that targeted NGS of a disease-specific subset of genes is equal to the quality of SS and it can therefore be reliably implemented as a stand-alone diagnostic test.
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Affiliation(s)
- Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
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van den Oever JME, Balkassmi S, Johansson LF, Adama van Scheltema PN, Suijkerbuijk RF, Hoffer MJV, Sinke RJ, Bakker E, Sikkema-Raddatz B, Boon EMJ. Successful Noninvasive Trisomy 18 Detection Using Single Molecule Sequencing. Clin Chem 2013; 59:705-9. [DOI: 10.1373/clinchem.2012.196212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND
Noninvasive trisomy 21 detection performed by use of massively parallel sequencing is achievable with high diagnostic sensitivity and low false-positive rates. Detection of fetal trisomy 18 and 13 has been reported as well but seems to be less accurate with the use of this approach. The reduced accuracy can be explained by PCR-introduced guanine-cytosine (GC) bias influencing sequencing data. Previously, we demonstrated that sequence data generated by single molecule sequencing show virtually no GC bias and result in a more pronounced noninvasive detection of fetal trisomy 21. In this study, single molecule sequencing was used for noninvasive detection of trisomy 18 and 13.
METHODS
Single molecule sequencing was performed on the Helicos platform with free DNA isolated from maternal plasma from 11 weeks of gestation onward (n = 17). Relative sequence tag density ratios were calculated against male control plasma samples and results were compared to those of previous karyotyping.
RESULTS
All trisomy 18 fetuses were identified correctly with a diagnostic sensitivity and specificity of 100%. However, low diagnostic sensitivity and specificity were observed for fetal trisomy 13 detection.
CONCLUSIONS
We successfully applied single molecule sequencing in combination with relative sequence tag density calculations for noninvasive trisomy 18 detection using free DNA from maternal plasma. However, noninvasive trisomy 13 detection was not accurate and seemed to be influenced by more than just GC content.
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Affiliation(s)
- Jessica ME van den Oever
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, the Netherlands
| | - Sahila Balkassmi
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, the Netherlands
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Ron F Suijkerbuijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mariëtte JV Hoffer
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, the Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Egbert Bakker
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, the Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elles MJ Boon
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, the Netherlands
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Duarri A, Jezierska J, Fokkens M, Meijer M, Schelhaas HJ, den Dunnen WFA, van Dijk F, Verschuuren-Bemelmans C, Hageman G, van de Vlies P, Küsters B, van de Warrenburg BP, Kremer B, Wijmenga C, Sinke RJ, Swertz MA, Kampinga HH, Boddeke E, Verbeek DS. Mutations in potassium channel kcnd3 cause spinocerebellar ataxia type 19. Ann Neurol 2013; 72:870-80. [PMID: 23280838 DOI: 10.1002/ana.23700] [Citation(s) in RCA: 99] [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: 04/05/2012] [Revised: 05/21/2012] [Accepted: 06/13/2012] [Indexed: 01/15/2023]
Abstract
OBJECTIVE To identify the causative gene for the neurodegenerative disorder spinocerebellar ataxia type 19 (SCA19) located on chromosomal region 1p21-q21. METHODS Exome sequencing was used to identify the causal mutation in a large SCA19 family. We then screened 230 ataxia families for mutations located in the same gene (KCND3, also known as Kv4.3) using high-resolution melting. SCA19 brain autopsy material was evaluated, and in vitro experiments using ectopic expression of wild-type and mutant Kv4.3 were used to study protein localization, stability, and channel activity by patch-clamping. RESULTS We detected a T352P mutation in the third extracellular loop of the voltage-gated potassium channel KCND3 that cosegregated with the disease phenotype in our original family. We identified 2 more novel missense mutations in the channel pore (M373I) and the S6 transmembrane domain (S390N) in 2 other ataxia families. T352P cerebellar autopsy material showed severe Purkinje cell degeneration, with abnormal intracellular accumulation and reduced protein levels of Kv4.3 in their soma. Ectopic expression of all mutant proteins in HeLa cells revealed retention in the endoplasmic reticulum and enhanced protein instability, in contrast to wild-type Kv4.3 that was localized on the plasma membrane. The regulatory β subunit Kv channel interacting protein 2 was able to rescue the membrane localization and the stability of 2 of the 3 mutant Kv4.3 complexes. However, this either did not restore the channel function of the membrane-located mutant Kv4.3 complexes or restored it only partially. INTERPRETATION KCND3 mutations cause SCA19 by impaired protein maturation and/or reduced channel function.
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Affiliation(s)
- Anna Duarri
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen
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Yuen WY, Sinke RJ, Jonkman MF. ITGB4-associated non-Herlitz junctional epidermolysis bullosa: report of two new cases carrying two novel ITGB4 mutations. Br J Dermatol 2012; 168:432-4. [PMID: 23013259 DOI: 10.1111/j.1365-2133.2012.11182.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yuen WY, Lemmink HH, van Dijk-Bos KK, Sinke RJ, Jonkman MF. Herlitz junctional epidermolysis bullosa: diagnostic features, mutational profile, incidence and population carrier frequency in the Netherlands. Br J Dermatol 2011; 165:1314-22. [PMID: 21801158 DOI: 10.1111/j.1365-2133.2011.10553.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Junctional epidermolysis bullosa, type Herlitz (JEB-H) is a lethal, autosomal recessive blistering disease caused by null mutations in the genes coding for the lamina lucida/densa adhesion protein laminin-332 (LAMB3, LAMA3 and LAMC2). OBJECTIVES To present the diagnostic features and molecular analyses of all 22 patients with JEB-H in the Dutch Epidermolysis Bullosa Registry between 1988 and 2011, and to calculate the disease incidence and carrier frequency in the Netherlands. METHODS All patients were analysed with immunofluorescence antigen mapping (IF), electron microscopy (EM) and molecular analysis. RESULTS The mean lifespan of our patients with JEB-H was 5·8 months (range 0·5-32·6). IF showed absent (91%) or strongly reduced (9%) staining for laminin-332 with monoclonal antibody GB3. In EM the hemidesmosomes and sub-basal dense plates were hypoplastic or absent. We identified mutations in all 22 patients: in 19 we found LAMB3 mutations, in two LAMA3 mutations, and in one LAMC2 mutations. We found three novel splice site mutations in LAMB3: (i) c.29-2A>G resulting in an out-of-frame skip of exon 3 and a premature termination codon (PTC); (ii) c.1289-2_1296del10 leading to an out-of-frame skip of exon 12 and a PTC; and (iii) c.3228+1G>T leading to an exon 21 skip. CONCLUSIONS All diagnostic tools should be evaluated to clarify the diagnosis of JEB-H. We have identified 11 different mutations in 22 patients with JEB-H, three of them novel. In the Netherlands the incidence rate of JEB-H is 4·0 per one million live births. The carrier frequency of a JEB-H mutation in the Dutch population is 1 in 249.
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Affiliation(s)
- W Y Yuen
- Department of Dermatology, Centre for Blistering Diseases, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, the Netherlands.
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Abstract
BACKGROUND Junctional epidermolysis bullosa of late onset (JEB-lo) is a rare disease characterized by blistering of primarily the hands and feet starting in childhood. The pathogenesis remains unclear. OBJECTIVES To clarify the pathogenesis of JEB-lo. METHODS Two patients with JEB-lo, a brother and a sister, were examined using electron microscopy (EM), immunofluorescence (IF) antigen mapping and molecular analysis. RESULTS We found subtle changes in IF antigen mapping and EM. The most remarkable changes were loss of the apical-lateral staining of monoclonal antibodies (mAbs) against type XVII collagen (Col17), and a broadened distribution of mAb staining against the ectodomain of Col17, laminin-332 and type VII collagen. Mutation analysis of COL17A1, encoding Col17, showed a compound heterozygosity for a novel mutation c.1992_1995delGGGT and the known mutation c.3908G>A in both patients. The deletion c.1992_1995delGGGT results in a premature termination codon and mRNA decay, leaving the patients functionally hemizygous for the missense mutation c.3908G>A (p.R1303Q) in the noncollagenous 4 domain of Col17. CONCLUSIONS JEB-lo is an autosomal recessive disorder caused by mutations in COL17A1, and subtle aberrations in EM and IF antigen mapping are clues to diagnosis.
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Affiliation(s)
- W Y Yuen
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Jongbloed JDH, Pósafalvi A, Kerstjens-Frederikse WS, Sinke RJ, van Tintelen JP. New clinical molecular diagnostic methods for congenital and inherited heart disease. ACTA ACUST UNITED AC 2010; 5:9-24. [DOI: 10.1517/17530059.2011.540566] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bakalkin G, Watanabe H, Jezierska J, Depoorter C, Verschuuren-Bemelmans C, Bazov I, Artemenko KA, Yakovleva T, Dooijes D, Van de Warrenburg BPC, Zubarev RA, Kremer B, Knapp PE, Hauser KF, Wijmenga C, Nyberg F, Sinke RJ, Verbeek DS. Prodynorphin mutations cause the neurodegenerative disorder spinocerebellar ataxia type 23. Am J Hum Genet 2010; 87:593-603. [PMID: 21035104 DOI: 10.1016/j.ajhg.2010.10.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [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: 08/06/2010] [Revised: 09/30/2010] [Accepted: 10/05/2010] [Indexed: 11/28/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are dominantly inherited neurodegenerative disorders characterized by progressive cerebellar ataxia and dysarthria. We have identified missense mutations in prodynorphin (PDYN) that cause SCA23 in four Dutch families displaying progressive gait and limb ataxia. PDYN is the precursor protein for the opioid neuropeptides, α-neoendorphin, and dynorphins A and B (Dyn A and B). Dynorphins regulate pain processing and modulate the rewarding effects of addictive substances. Three mutations were located in Dyn A, a peptide with both opioid activities and nonopioid neurodegenerative actions. Two of these mutations resulted in excessive generation of Dyn A in a cellular model system. In addition, two of the mutant Dyn A peptides induced toxicity above that of wild-type Dyn A in cultured striatal neurons. The fourth mutation was located in the nonopioid PDYN domain and was associated with altered expression of components of the opioid and glutamate system, as evident from analysis of SCA23 autopsy tissue. Thus, alterations in Dyn A activities and/or impairment of secretory pathways by mutant PDYN may lead to glutamate neurotoxicity, which underlies Purkinje cell degeneration and ataxia. PDYN mutations are identified in a small subset of ataxia families, indicating that SCA23 is an infrequent SCA type (∼0.5%) in the Netherlands and suggesting further genetic SCA heterogeneity.
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Affiliation(s)
- Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Sweden
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Vorstman JA, Chow EW, Ophoff RA, van Engeland H, Beemer FA, Kahn RS, Sinke RJ, Bassett AS. Association of the PIK4CA schizophrenia-susceptibility gene in adults with the 22q11.2 deletion syndrome. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:430-3. [PMID: 18646052 PMCID: PMC3127866 DOI: 10.1002/ajmg.b.30827] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 22q11.2 deletion syndrome (22q11DS) is associated with an increased prevalence (20-30%) of schizophrenia. Therefore, it is likely that one or more genes within the 22q11.2 region are causally related to schizophrenia. Recently, a significant association with schizophrenia in the general population was reported for three SNPs in phosphatidyl-inositol-4-kinase-catalytic-alpha (PIK4CA), a gene located in the 22q11.2 region. In the current study, we tested the hypothesis that the same PIK4CA risk-alleles would be associated with schizophrenia in individuals with 22q11DS. Our analysis of the PIK4CA genotypes in a sample of 79 adults with typical 22q11.2 deletions, comparing those with schizophrenia to those without, revealed a significant association. Our findings represent an independent replication of the previously reported PIK4CA association with schizophrenia in the general population. Second, the results of this study indicate that variation at PIK4CA may be a relevant factor influencing the risk of schizophrenia in individuals with 22q11DS.
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Affiliation(s)
- Jacob A.S. Vorstman
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands,Correspondence to: Jacob A.S. Vorstman, Heidelberglaan 100, Utrecht 3584CX, The Netherlands.
| | - Eva W. Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada, Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Roel A. Ophoff
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands, Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, University Medical Center Utrecht, Utrecht, The Netherlands, Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California
| | - Herman van Engeland
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Frits A. Beemer
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - René S. Kahn
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Richard J. Sinke
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada, Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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49
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Zhou K, Dempfle A, Arcos-Burgos M, Bakker SC, Banaschewski T, Biederman J, Buitelaar J, Castellanos F, Doyle A, Ebstein RP, Ekholm J, Forabosco P, Franke B, Freitag C, Friedel S, Gill M, Hebebrand J, Hinney A, Jacob C, Lesch KP, Loo SK, Lopera F, McCracken JT, McGough JJ, Meyer J, Mick E, Miranda A, Muenke M, Mulas F, Nelson SF, Nguyen T, Oades RD, Ogdie MN, Palacio JD, Pineda D, Reif A, Renner TJ, Roeyers H, Romanos M, Rothenberger A, Schäfer H, Sergeant J, Sinke RJ, Smalley SL, Sonuga-Barke E, Steinhausen HC, van der Meulen E, Walitza S, Warnke A, Lewis CM, Faraone SV, Asherson P. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1392-8. [PMID: 18988193 PMCID: PMC2890047 DOI: 10.1002/ajmg.b.30878] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [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] [Indexed: 12/25/2022]
Abstract
Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies, there has been limited replications between the various independent datasets. The current study gathered the results from all seven of the ADHD linkage scans and performed a Genome Scan Meta Analysis (GSMA) to identify the genomic region with most consistent linkage evidence across the studies. Genome-wide significant linkage (P(SR) = 0.00034, P(OR) = 0.04) was identified on chromosome 16 between 64 and 83 Mb. In addition there are nine other genomic regions from the GSMA showing nominal or suggestive evidence of linkage. All these linkage results may be informative and focus the search for novel ADHD susceptibility genes.
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Affiliation(s)
- Kaixin Zhou
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Astrid Dempfle
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Mauricio Arcos-Burgos
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven C. Bakker
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany
| | - Joseph Biederman
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Jan Buitelaar
- Department of Psychiatry, Radboud University Nijmegen, Donders Centre for Neuroscience, Medical Centre, Nijmegen, The Netherlands
| | | | - Alysa Doyle
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jenny Ekholm
- Department of Human Genetics, UCLA, Los Angeles, California
| | - Paola Forabosco
- Department of Medical and Molecular Genetics, King's College London, London, UK
- Istituto di Genetica delle Popolazioni—CNR, Alghero, Italy
| | - Barbara Franke
- Department of Psychiatry, Radboud University Nijmegen, Donders Centre for Neuroscience, Medical Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christine Freitag
- Department of Child and Adolescent Psychiatry, Saarland University Hospital, Homburg, Germany
| | - Susann Friedel
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Christian Jacob
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Klaus Peter Lesch
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Sandra K. Loo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Francisco Lopera
- Neurosciences Group, University of Antioquia, Medellín, Colombia
| | - James T. McCracken
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - James J. McGough
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Jobst Meyer
- Department of Neurobehavioral Genetics, University of Trier, Trier, Germany
| | - Eric Mick
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Ana Miranda
- Department of Developmental and Educational Psychology, University of Valencia, Valencia, Spain
| | - Maximilian Muenke
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Fernando Mulas
- Department of Neuropaediatric, La Fe University Hospital, Faculty of Medicine, Valencia, Spain
| | | | - T.Trang Nguyen
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Robert D. Oades
- University Clinic for Child and Adolescent Psychiatry, Essen, Germany
| | | | | | - David Pineda
- Neurosciences Group, University of Antioquia, Medellín, Colombia
| | - Andreas Reif
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Tobias J. Renner
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | | | - Marcel Romanos
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | | | - Helmut Schäfer
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Joseph Sergeant
- Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands
| | - Richard J. Sinke
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan L. Smalley
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Edmund Sonuga-Barke
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Child Study Center, New York University, New York, New York
- School of Psychology, Institute for Disorder on Impulse and Attention, University of Southampton, Highfield, Southampton, UK
| | | | - Emma van der Meulen
- Department of Child and Adolescent Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susanne Walitza
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Andreas Warnke
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Cathryn M Lewis
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Stephen V. Faraone
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York
| | - Philip Asherson
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
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50
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Jungerius BJ, Hoogendoorn MLC, Bakker SC, Van't Slot R, Bardoel AF, Ophoff RA, Wijmenga C, Kahn RS, Sinke RJ. An association screen of myelin-related genes implicates the chromosome 22q11 PIK4CA gene in schizophrenia. Mol Psychiatry 2008; 13:1060-8. [PMID: 17893707 DOI: 10.1038/sj.mp.4002080] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Several lines of evidence, including expression analyses, brain imaging and genetic studies suggest that the integrity of myelin is disturbed in schizophrenia patients. In this study, we first reconstructed a pathway of 138 myelin-related genes, all involved in myelin structure, composition, development or maintenance. Then we performed a two-stage association analysis on these 138 genes using 771 single nucleotide polymorphisms (SNPs). Analysis of our data from 310 cases vs 880 controls demonstrated association of 10 SNPs from six genes. Specifically, we observed highly significant P-values for association in PIK4CA (observed P=6.1 x 10(-6)). These findings remained significant after Bonferroni correction for 771 tests. The PIK4CA gene is located in the chromosome 22q11 deletion syndrome region, which is of particular interest because it has been implicated in schizophrenia. We also report weak association of SNPs in PIK3C2G, FGF1, FGFR1, ARHGEF10 and PSAP (observed P<or=0.01). Our approach--of screening genes involved in a particular pathway for association--resulted in identification of several, mostly novel, genes associated with the risk of developing schizophrenia in the Dutch population.
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Affiliation(s)
- B J Jungerius
- Complex Genetics Section, DBG-Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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