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Kaiyrzhanov R, Ortigoza-Escobar JD, Stringer BW, Ganieva M, Gowda VK, Srinivasan VM, Macaya A, Laner A, Onbool E, Al-Shammari R, Al-Owain M, Deconinck N, Vilain C, Dontaine P, Self E, Akram R, Hussain G, Baig SM, Iqbal J, Salpietro V, Neshatdoust M, Kasiri M, Yesil G, Uygur T, Pysden K, Berry IR, Alves CA, Giacomotto J, Houlden H, Maroofian R. Clinical and Molecular Spectrum of Autosomal Recessive CA8-Related Cerebellar Ataxia. Mov Disord 2024. [PMID: 38581205 DOI: 10.1002/mds.29754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Based on a limited number of reported families, biallelic CA8 variants have currently been associated with a recessive neurological disorder named, cerebellar ataxia, mental retardation, and dysequilibrium syndrome 3 (CAMRQ-3). OBJECTIVES We aim to comprehensively investigate CA8-related disorders (CA8-RD) by reviewing existing literature and exploring neurological, neuroradiological, and molecular observations in a cohort of newly identified patients. METHODS We analyzed the phenotype of 27 affected individuals from 14 families with biallelic CA8 variants (including data from 15 newly identified patients from eight families), ages 4 to 35 years. Clinical, genetic, and radiological assessments were performed, and zebrafish models with ca8 knockout were used for functional analysis. RESULTS Patients exhibited varying degrees of neurodevelopmental disorders (NDD), along with predominantly progressive cerebellar ataxia and pyramidal signs and variable bradykinesia, dystonia, and sensory impairment. Quadrupedal gait was present in only 10 of 27 patients. Progressive selective cerebellar atrophy, predominantly affecting the superior vermis, was a key diagnostic finding in all patients. Seven novel homozygous CA8 variants were identified. Zebrafish models demonstrated impaired early neurodevelopment and motor behavior on ca8 knockout. CONCLUSION Our comprehensive analysis of phenotypic features indicates that CA8-RD exhibits a wide range of clinical manifestations, setting it apart from other subtypes within the category of CAMRQ. CA8-RD is characterized by cerebellar atrophy and should be recognized as part of the autosomal-recessive cerebellar ataxias associated with NDD. Notably, the presence of progressive superior vermis atrophy serves as a valuable diagnostic indicator. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Juan Darío Ortigoza-Escobar
- U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
- Movement Disorders Unit, Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Brett W Stringer
- Griffith Institute for Drug Discovery, Centre for Cellular Phenomics, School of Environment and Science Griffith University, Brisbane, Queensland, Australia
| | - Manizha Ganieva
- Avicenna Tajik State Medical University, Department of Neurology and Medical Genetics, Dushanbe, Tajikistan
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Alfons Macaya
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
- Department of Paediatric Neurology, University Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Enas Onbool
- Neurology department, King Abdulaziz Specialist Hospital, Skaka Aljouf, Saudi Arabia
| | - Randa Al-Shammari
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Nicolas Deconinck
- Centre de Référence des Maladies Neuromusculaires et Service de Neurologie Pédiatrique, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire Reine Fabiola (HUDERF); Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pauline Dontaine
- Centre de Référence des Maladies Neuromusculaires et Service de Neurologie Pédiatrique, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Eleanor Self
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Rabia Akram
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- Neurochemical biology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Ghulam Hussain
- Neurochemical biology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, Faisalabad, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Javed Iqbal
- Department of Neurology, Allied Hospital, Faisalabad Medical University, Faisalabad, Pakistan
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Maedeh Neshatdoust
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mahboubeh Kasiri
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Turkan Uygur
- Department of Pediatric Neurology, Bezmialem Vakif University, İstanbul, Turkey
| | - Karen Pysden
- Paediatric Neurology Department, Leeds Teaching Hospitals, Leeds General Infirmary, Leeds, United Kingdom
| | - Ian R Berry
- Yorkshire and North East Genomic Laboratory Hub Central Laboratory, Leeds, United Kingdom
| | - Cesar Augusto Alves
- Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jean Giacomotto
- Griffith Institute for Drug Discovery, Centre for Cellular Phenomics, School of Environment and Science Griffith University, Brisbane, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
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Loong L, Garrett A, Allen S, Choi S, Durkie M, Callaway A, Drummond J, Burghel GJ, Robinson R, Torr B, Berry IR, Wallace AJ, Eccles DM, Ellard S, Baple E, Evans DG, Woodward ER, Kulkarni A, Lalloo F, Tischkowitz M, Lucassen A, Hanson H, Turnbull C. Reclassification of clinically-detected sequence variants: Framework for genetic clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group UK). Genet Med 2022; 24:1867-1877. [PMID: 35657381 DOI: 10.1016/j.gim.2022.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Variant classifications may change over time, driven by emergence of fresh or contradictory evidence or evolution in weighing or combination of evidence items. For variant classifications above the actionability threshold, which is classification of likely pathogenic or pathogenic, clinical actions may be irreversible, such as risk-reducing surgery or prenatal interventions. Variant reclassification up or down across the actionability threshold can therefore have significant clinical consequences. Laboratory approaches to variant reinterpretation and reclassification vary widely. METHODS Cancer Variant Interpretation Group UK is a multidisciplinary network of clinical scientists and genetic clinicians from across the 24 Molecular Diagnostic Laboratories and Clinical Genetics Services of the United Kingdom (NHS) and Republic of Ireland. We undertook surveys, polls, and national meetings of Cancer Variant Interpretation Group UK to evaluate opinions about clinical and laboratory management regarding variant reclassification. RESULTS We generated a consensus framework on variant reclassification applicable to cancer susceptibility genes and other clinical areas, which provides explicit recommendations for clinical and laboratory management of variant reclassification scenarios on the basis of the nature of the new evidence, the magnitude of evidence shift, and the final classification score. CONCLUSION In this framework, clinical and laboratory resources are targeted for maximal clinical effect and minimal patient harm, as appropriate to all resource-constrained health care settings.
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Affiliation(s)
- Lucy Loong
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Subin Choi
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NHS North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, United Kingdom
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Central and South Genomics Laboratory Hub, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
| | - James Drummond
- Cambridge Genomic Laboratory, East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - George J Burghel
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Rachel Robinson
- North East and Yorkshire Genomic Laboratory Hub, The Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Beth Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Ian R Berry
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sian Ellard
- Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; University of Exeter Medical School, Exeter, United Kingdom
| | - Emma Baple
- University of Exeter Medical School, Exeter, United Kingdom; Genomics England, London, United Kingdom
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Division of Evolution & Genomic Sciences, The University of Manchester, Manchester, United Kingdom
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Division of Evolution & Genomic Sciences, The University of Manchester, Manchester, United Kingdom
| | - Anjana Kulkarni
- Southeast Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Anneke Lucassen
- Wellcome Centre for Human Genetics/Centre for Personalised Medicine, University of Oxford, Oxford, United Kingdom; Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Helen Hanson
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Department of Clinical Genetics, St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom.
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3
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Loong L, Cubuk C, Choi S, Allen S, Torr B, Garrett A, Loveday C, Durkie M, Callaway A, Burghel GJ, Drummond J, Robinson R, Berry IR, Wallace A, Eccles DM, Tischkowitz M, Ellard S, Ware JS, Hanson H, Turnbull C. Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants. Genet Med 2021; 24:552-563. [PMID: 34906453 PMCID: PMC8896276 DOI: 10.1016/j.gim.2021.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/04/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice. METHODS We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset. RESULTS pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62. CONCLUSION These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met.
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Affiliation(s)
- Lucy Loong
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Cankut Cubuk
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Subin Choi
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Beth Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Chey Loveday
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NHS North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, United Kingdom
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, United Kingdom; Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - George J Burghel
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - James Drummond
- East Genomic Laboratory Hub, Cambridge University Hospitals Genomic Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Rachel Robinson
- North East and Yorkshire Genomic Laboratory Hub, The Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Ian R Berry
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, NIHR Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - James S Ware
- National Heart and Lung Institute, Faculty of Medicine, and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Helen Hanson
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Department of Clinical Genetics, St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom.
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Whitehouse LLE, Smith CEL, Poulter JA, Brown CJ, Patel A, Lamb T, Brown LR, O'Sullivan EA, Mitchell RE, Berry IR, Charlton R, Inglehearn CF, Mighell AJ. NOVEL DLX3 VARIANTS IN AMELOGENESIS IMPERFECTA WITH ATTENUATED TRICHO-DENTO-OSSEOUS SYNDROME. Oral Surg Oral Med Oral Pathol Oral Radiol 2021. [DOI: 10.1016/j.oooo.2021.03.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Nikolopoulos G, Smith CEL, Poulter JA, Murillo G, Silva S, Lamb T, Berry IR, Brown CJ, Day PF, Soldani F, Al-Bahlani S, Harris SA, O'Connell MJ, Inglehearn CF, Mighell AJ. Spectrum of pathogenic variants and founder effects in amelogenesis imperfecta associated with MMP20. Hum Mutat 2021; 42:567-576. [PMID: 33600052 DOI: 10.1002/humu.24187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 11/12/2022]
Abstract
Amelogenesis imperfecta (AI) describes a heterogeneous group of developmental enamel defects that typically have Mendelian inheritance. Exome sequencing of 10 families with recessive hypomaturation AI revealed four novel and one known variants in the matrix metallopeptidase 20 (MMP20) gene that were predicted to be pathogenic. MMP20 encodes a protease that cleaves the developing extracellular enamel matrix and is necessary for normal enamel crystal growth during amelogenesis. New homozygous missense changes were shared between four families of Pakistani heritage (c.625G>C; p.(Glu209Gln)) and two of Omani origin (c.710C>A; p.(Ser237Tyr)). In two families of UK origin and one from Costa Rica, affected individuals were homozygous for the previously reported c.954-2A>T; p.(Ile319Phefs*19) variant. For each of these variants, microsatellite haplotypes appeared to exclude a recent founder effect, but elements of haplotype were conserved, suggesting more distant founding ancestors. New compound heterozygous changes were identified in one family of the European heritage: c.809_811+12delinsCCAG; p.(?) and c.1122A>C; p.(Gln374His). This report further elucidates the mutation spectrum of MMP20 and the probable impact on protein function, confirms a consistent hypomaturation phenotype and shows that mutations in MMP20 are a common cause of autosomal recessive AI in some communities.
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Affiliation(s)
- Georgios Nikolopoulos
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK.,Department of Oral Biology, School of Dentistry, St James's University Hospital, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Gina Murillo
- School of Dentistry, Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro Montes De Oca, Costa Rica
| | - Sandra Silva
- Cellular and Molecular Biology Centre (CBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro Montes De Oca, Costa Rica
| | - Teresa Lamb
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ian R Berry
- Leeds Genetics Laboratory, St James's University Hospital, Leeds, UK
| | | | - Peter F Day
- Department of Paediatric Dentistry, Leeds Dental Institute, University of Leeds, Leeds, UK.,Community Dental Service, Horton Park Health Centre, Bradford District Care NHS Foundation Trust, Bradford, UK
| | - Francesca Soldani
- Community Dental Service, Horton Park Health Centre, Bradford District Care NHS Foundation Trust, Bradford, UK
| | - Suhaila Al-Bahlani
- Dental & O.M.F.S Clinic, Al Nahdha Hospital, Ministry of Health, Muscat, Oman
| | - Sarah A Harris
- School of Physics, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mary J O'Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Alan J Mighell
- Department of Oral Biology, School of Dentistry, St James's University Hospital, University of Leeds, Leeds, UK
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Garrett A, Durkie M, Callaway A, Burghel GJ, Robinson R, Drummond J, Torr B, Cubuk C, Berry IR, Wallace AJ, Ellard S, Eccles DM, Tischkowitz M, Hanson H, Turnbull C. Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations. J Med Genet 2020; 58:297-304. [PMID: 33208383 PMCID: PMC8086256 DOI: 10.1136/jmedgenet-2020-107248] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
Accurate classification of variants in cancer susceptibility genes (CSGs) is key for correct estimation of cancer risk and management of patients. Consistency in the weighting assigned to individual elements of evidence has been much improved by the American College of Medical Genetics (ACMG) 2015 framework for variant classification, UK Association for Clinical Genomic Science (UK-ACGS) Best Practice Guidelines and subsequent Cancer Variant Interpretation Group UK (CanVIG-UK) consensus specification for CSGs. However, considerable inconsistency persists regarding practice in the combination of evidence elements. CanVIG-UK is a national subspecialist multidisciplinary network for cancer susceptibility genomic variant interpretation, comprising clinical scientist and clinical geneticist representation from each of the 25 diagnostic laboratories/clinical genetic units across the UK and Republic of Ireland. Here, we summarise the aggregated evidence elements and combinations possible within different variant classification schemata currently employed for CSGs (ACMG, UK-ACGS, CanVIG-UK and ClinGen gene-specific guidance for PTEN, TP53 and CDH1). We present consensus recommendations from CanVIG-UK regarding (1) consistent scoring for combinations of evidence elements using a validated numerical 'exponent score' (2) new combinations of evidence elements constituting likely pathogenic' and 'pathogenic' classification categories, (3) which evidence elements can and cannot be used in combination for specific variant types and (4) classification of variants for which there are evidence elements for both pathogenicity and benignity.
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Affiliation(s)
- Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, Wiltshire, UK.,Human Genetics and Genomic Medicine, University of Southampton Faculty of Medicine, Southampton, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, Cambridgeshire, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Cankut Cubuk
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Ian R Berry
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Diana M Eccles
- Cancer Sciences Research Group, University of Southampton Faculty of Medicine, Southampton, UK
| | - Marc Tischkowitz
- Department of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Helen Hanson
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK .,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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7
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Garrett A, Callaway A, Durkie M, Cubuk C, Alikian M, Burghel GJ, Robinson R, Izatt L, Talukdar S, Side L, Cranston T, Palmer-Smith S, Baralle D, Berry IR, Drummond J, Wallace AJ, Norbury G, Eccles DM, Ellard S, Lalloo F, Evans DG, Woodward E, Tischkowitz M, Hanson H, Turnbull C. Cancer Variant Interpretation Group UK (CanVIG-UK): an exemplar national subspecialty multidisciplinary network. J Med Genet 2020; 57:829-834. [PMID: 32170000 PMCID: PMC7691806 DOI: 10.1136/jmedgenet-2019-106759] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 12/04/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Advances in technology have led to a massive expansion in the capacity for genomic analysis, with a commensurate fall in costs. The clinical indications for genomic testing have evolved markedly; the volume of clinical sequencing has increased dramatically; and the range of clinical professionals involved in the process has broadened. There is general acceptance that our early dichotomous paradigms of variants being pathogenic–high risk and benign–no risk are overly simplistic. There is increasing recognition that the clinical interpretation of genomic data requires significant expertise in disease–gene-variant associations specific to each disease area. Inaccurate interpretation can lead to clinical mismanagement, inconsistent information within families and misdirection of resources. It is for this reason that ‘national subspecialist multidisciplinary meetings’ (MDMs) for genomic interpretation have been articulated as key for the new NHS Genomic Medicine Service, of which Cancer Variant Interpretation Group UK (CanVIG-UK) is an early exemplar. CanVIG-UK was established in 2017 and now has >100 UK members, including at least one clinical diagnostic scientist and one clinical cancer geneticist from each of the 25 regional molecular genetics laboratories of the UK and Ireland. Through CanVIG-UK, we have established national consensus around variant interpretation for cancer susceptibility genes via monthly national teleconferenced MDMs and collaborative data sharing using a secure online portal. We describe here the activities of CanVIG-UK, including exemplar outputs and feedback from the membership.
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Affiliation(s)
- Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, UK.,Human Genetics and Genomic Medicin, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Cankut Cubuk
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mary Alikian
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Louise Izatt
- Department of Clinical Genetics, Guy's and Saint Thomas' NHS Foundation Trust, London, UK
| | - Sabrina Talukdar
- Department of Clinical Genetics, Saint George's University Hospitals NHS Foundation Trust, London, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Treena Cranston
- Oxford Molecular Genetics Laboratory, Churchill Hospital, Oxford, UK
| | | | - Diana Baralle
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ian R Berry
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gail Norbury
- Regional Genetics Service, Guy's and Saint Thomas' NHS Foundation Trust, London, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Emma Woodward
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health, Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Helen Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK.,Department of Clinical Genetics, Saint George's University Hospitals NHS Foundation Trust, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK .,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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8
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Lenk GM, Berry IR, Stutterd CA, Blyth M, Green L, Vadlamani G, Warren D, Craven I, Fanjul-Fernandez M, Rodriguez-Casero V, Lockhart PJ, Vanderver A, Simons C, Gibb S, Sadedin S, White SM, Christodoulou J, Skibina O, Ruddle J, Tan TY, Leventer RJ, Livingston JH, Meisler MH. Cerebral hypomyelination associated with biallelic variants of FIG4. Hum Mutat 2019; 40:619-630. [PMID: 30740813 DOI: 10.1002/humu.23720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 08/21/2018] [Revised: 12/11/2018] [Accepted: 02/06/2019] [Indexed: 01/07/2023]
Abstract
The lipid phosphatase gene FIG4 is responsible for Yunis-Varón syndrome and Charcot-Marie-Tooth disease Type 4J, a peripheral neuropathy. We now describe four families with FIG4 variants and prominent abnormalities of central nervous system (CNS) white matter (leukoencephalopathy), with onset in early childhood, ranging from severe hypomyelination to mild undermyelination, in addition to peripheral neuropathy. Affected individuals inherited biallelic FIG4 variants from heterozygous parents. Cultured fibroblasts exhibit enlarged vacuoles characteristic of FIG4 dysfunction. Two unrelated families segregate the same G > A variant in the +1 position of intron 21 in the homozygous state in one family and compound heterozygous in the other. This mutation in the splice donor site of exon 21 results in read-through from exon 20 into intron 20 and truncation of the final 115 C-terminal amino acids of FIG4, with retention of partial function. The observed CNS white matter disorder in these families is consistent with the myelination defects in the FIG4 null mouse and the known role of FIG4 in oligodendrocyte maturation. The families described here the expanded clinical spectrum of FIG4 deficiency to include leukoencephalopathy.
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Affiliation(s)
- Guy M Lenk
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Ian R Berry
- Leeds Genetics Laboratory, The Leeds Teaching Hospitals NHS Trust, St James's University Hospital, Leeds, UK
| | - Chloe A Stutterd
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Royal Children's Hospital, Melbourne, Australia
| | - Moira Blyth
- Yorkshire Regional Genetics Service, The Leeds Teaching Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Lydia Green
- Paediatric Neurology, The Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Gayatri Vadlamani
- Paediatric Neurology, The Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Daniel Warren
- The Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Ian Craven
- The Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Miriam Fanjul-Fernandez
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | - Paul J Lockhart
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia and Perlman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Australia.,Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Susan Gibb
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Royal Children's Hospital, Melbourne, Australia
| | - Simon Sadedin
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | - Susan M White
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Olga Skibina
- Eastern Health Neurosciences, Box Hill Hospital, Monash University, Melbourne, Australia
| | - Jonathan Ruddle
- Royal Children's Hospital, Melbourne, Australia.,Centre for Eye Research Australia Ltd, East Melbourne, Victoria, Australia.,Department of Ophthalmology, University of Melbourne, Melbourne, Australia
| | - Tiong Y Tan
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Richard J Leventer
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Royal Children's Hospital, Melbourne, Australia
| | - John H Livingston
- Paediatric Neurology, The Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
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9
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Lord J, McMullan DJ, Eberhardt RY, Rinck G, Hamilton SJ, Quinlan-Jones E, Prigmore E, Keelagher R, Best SK, Carey GK, Mellis R, Robart S, Berry IR, Chandler KE, Cilliers D, Cresswell L, Edwards SL, Gardiner C, Henderson A, Holden ST, Homfray T, Lester T, Lewis RA, Newbury-Ecob R, Prescott K, Quarrell OW, Ramsden SC, Roberts E, Tapon D, Tooley MJ, Vasudevan PC, Weber AP, Wellesley DG, Westwood P, White H, Parker M, Williams D, Jenkins L, Scott RH, Kilby MD, Chitty LS, Hurles ME, Maher ER. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet 2019; 393:747-757. [PMID: 30712880 PMCID: PMC6386638 DOI: 10.1016/s0140-6736(18)31940-8] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). METHODS In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. FINDINGS The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4-11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). INTERPRETATION WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. FUNDING UK Department of Health and Social Care and The Wellcome Trust.
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Affiliation(s)
| | - Dominic J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | | | | | - Susan J Hamilton
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Elizabeth Quinlan-Jones
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Rebecca Keelagher
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Sunayna K Best
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Georgina K Carey
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Rhiannon Mellis
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Sarah Robart
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Ian R Berry
- The Leeds Genetics Laboratory, St James's University Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Deirdre Cilliers
- Oxford Genomic Medicine Centre, Nuffield Orthopaedic Centre, Oxford, UK
| | - Lara Cresswell
- Department of Cytogenetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Sandra L Edwards
- Cytogenetics Service, Norfolk and Norwich University Hospital Foundation Trust, Norwich, UK
| | - Carol Gardiner
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Simon T Holden
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Centre, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Tracy Lester
- Oxford Regional Genetics Services, The Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rebecca A Lewis
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Katrina Prescott
- Chapel Allerton Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Oliver W Quarrell
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Eileen Roberts
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Dagmar Tapon
- Centre for Fetal Care, Queen Charlotte's and Chelsea Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Madeleine J Tooley
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Astrid P Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Diana G Wellesley
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul Westwood
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Helen White
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Richard H Scott
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Mark D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | | | - Eamonn R Maher
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK; Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, UK.
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10
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Hartill VL, van de Hoek G, Patel MP, Little R, Watson CM, Berry IR, Shoemark A, Abdelmottaleb D, Parkes E, Bacchelli C, Szymanska K, Knoers NV, Scambler PJ, Ueffing M, Boldt K, Yates R, Winyard PJ, Adler B, Moya E, Hattingh L, Shenoy A, Hogg C, Sheridan E, Roepman R, Norris D, Mitchison HM, Giles RH, Johnson CA. DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport. Hum Mol Genet 2019; 27:529-545. [PMID: 29228333 PMCID: PMC5886296 DOI: 10.1093/hmg/ddx422] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 01/11/2023] Open
Abstract
DNAAF1 (LRRC50) is a cytoplasmic protein required for dynein heavy chain assembly and cilia motility, and DNAAF1 mutations cause primary ciliary dyskinesia (PCD; MIM 613193). We describe four families with DNAAF1 mutations and complex congenital heart disease (CHD). In three families, all affected individuals have typical PCD phenotypes. However, an additional family demonstrates isolated CHD (heterotaxy) in two affected siblings, but no clinical evidence of PCD. We identified a homozygous DNAAF1 missense mutation, p.Leu191Phe, as causative for heterotaxy in this family. Genetic complementation in dnaaf1-null zebrafish embryos demonstrated the rescue of normal heart looping with wild-type human DNAAF1, but not the p.Leu191Phe variant, supporting the conserved pathogenicity of this DNAAF1 missense mutation. This observation points to a phenotypic continuum between CHD and PCD, providing new insights into the pathogenesis of isolated CHD. In further investigations of the function of DNAAF1 in dynein arm assembly, we identified interactions with members of a putative dynein arm assembly complex. These include the ciliary intraflagellar transport protein IFT88 and the AAA+ (ATPases Associated with various cellular Activities) family proteins RUVBL1 (Pontin) and RUVBL2 (Reptin). Co-localization studies support these findings, with the loss of RUVBL1 perturbing the co-localization of DNAAF1 with IFT88. We show that RUVBL1 orthologues have an asymmetric left-sided distribution at both the mouse embryonic node and the Kupffer's vesicle in zebrafish embryos, with the latter asymmetry dependent on DNAAF1. These results suggest that DNAAF1-RUVBL1 biochemical and genetic interactions have a novel functional role in symmetry breaking and cardiac development.
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Affiliation(s)
- Verity L Hartill
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Glenn van de Hoek
- Department of Nephrology and Hypertension.,Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Mitali P Patel
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Rosie Little
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Christopher M Watson
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Ian R Berry
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Amelia Shoemark
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK.,School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Dina Abdelmottaleb
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK.,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Emma Parkes
- Manchester Royal Infirmary, Manchester M13 9WL, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Katarzyna Szymanska
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Nine V Knoers
- Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Peter J Scambler
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Marius Ueffing
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Karsten Boldt
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Robert Yates
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Paediatric Cardiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Paul J Winyard
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Beryl Adler
- Department of Paediatrics, Luton and Dunstable Hospital NHS Trust, Luton LU4 0DZ, UK
| | - Eduardo Moya
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Louise Hattingh
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Anil Shenoy
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Claire Hogg
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Eamonn Sheridan
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, The Netherlands
| | - Dominic Norris
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | | | - Colin A Johnson
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
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11
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Whitehouse LLE, Smith CEL, Poulter JA, Brown CJ, Patel A, Lamb T, Brown LR, O’Sullivan EA, Mitchell RE, Berry IR, Charlton R, Inglehearn CF, Mighell AJ. Novel DLX3 variants in amelogenesis imperfecta with attenuated tricho-dento-osseous syndrome. Oral Dis 2019; 25:182-191. [PMID: 30095208 PMCID: PMC6334507 DOI: 10.1111/odi.12955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/16/2018] [Revised: 07/12/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Variants in DLX3 cause tricho-dento-osseous syndrome (TDO, MIM #190320), a systemic condition with hair, nail and bony changes, taurodontism and amelogenesis imperfecta (AI), inherited in an autosomal dominant fashion. Different variants found within this gene are associated with different phenotypic presentations. To date, six different DLX3 variants have been reported in TDO. The aim of this paper was to explore and discuss three recently uncovered new variants in DLX3. SUBJECTS AND METHODS Whole-exome sequencing identified a new DLX3 variant in one family, recruited as part of an ongoing study of genetic variants associated with AI. Targeted clinical exome sequencing of two further families revealed another new variant of DLX3 and complete heterozygous deletion of DLX3. For all three families, the phenotypes were shown to consist of AI and taurodontism, together with other attenuated features of TDO. RESULTS c.574delG p.(E192Rfs*66), c.476G>T (p.R159L) and a heterozygous deletion of the entire DLX3 coding region were identified in our families. CONCLUSION These previously unreported variants add to the growing literature surrounding AI, allowing for more accurate genetic testing and better understanding of the associated clinical consequences.
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Affiliation(s)
| | - Claire E. L. Smith
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical SciencesUniversity of LeedsLeedsUK
| | | | | | - Anesha Patel
- Birmingham Dental Hospital and School of DentistryBirminghamUK
| | - Teresa Lamb
- Oxford University Hospitals NHS Foundation TrustOxfordUK
| | | | | | | | - Ian R. Berry
- Leeds Genetics LaboratorySt James’s University HospitalLeedsUK
| | - Ruth Charlton
- Leeds Genetics LaboratorySt James’s University HospitalLeedsUK
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical SciencesUniversity of LeedsLeedsUK
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12
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Boudin E, de Jong TR, Prickett TCR, Lapauw B, Toye K, Van Hoof V, Luyckx I, Verstraeten A, Heymans HSA, Dulfer E, Van Laer L, Berry IR, Dobbie A, Blair E, Loeys B, Espiner EA, Wit JM, Van Hul W, Houpt P, Mortier GR. Bi-allelic Loss-of-Function Mutations in the NPR-C Receptor Result in Enhanced Growth and Connective Tissue Abnormalities. Am J Hum Genet 2018; 103:288-295. [PMID: 30032985 DOI: 10.1016/j.ajhg.2018.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
The natriuretic peptide signaling pathway has been implicated in many cellular processes, including endochondral ossification and bone growth. More precisely, different mutations in the NPR-B receptor and the CNP ligand have been identified in individuals with either short or tall stature. In this study we show that the NPR-C receptor (encoded by NPR3) is also important for the regulation of linear bone growth. We report four individuals, originating from three different families, with a phenotype characterized by tall stature, long digits, and extra epiphyses in the hands and feet. In addition, aortic dilatation was observed in two of these families. In each affected individual, we identified a bi-allelic loss-of-function mutation in NPR3. The missense mutations (c.442T>C [p.Ser148Pro] and c.1088A>T [p.Asp363Val]) resulted in intracellular retention of the NPR-C receptor and absent localization on the plasma membrane, whereas the nonsense mutation (c.1524delC [p.Tyr508∗]) resulted in nonsense-mediated mRNA decay. Biochemical analysis of plasma from two affected and unrelated individuals revealed a reduced NTproNP/NP ratio for all ligands and also high cGMP levels. These data strongly suggest a reduced clearance of natriuretic peptides by the defective NPR-C receptor and consequently increased activity of the NPR-A/B receptors. In conclusion, this study demonstrates that loss-of-function mutations in NPR3 result in increased NPR-A/B signaling activity and cause a phenotype marked by enhanced bone growth and cardiovascular abnormalities.
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Affiliation(s)
- Eveline Boudin
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Tjeerd R de Jong
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Isala Clinics, 8025 AB Zwolle, the Netherlands
| | - Tim C R Prickett
- Department of Medicine, University of Otago, Christchurch 8011, New Zealand
| | - Bruno Lapauw
- Department of Endocrinology and Unit for Osteoporosis and Metabolic Bone Diseases, Ghent University Hospital, 9000 Ghent, Belgium
| | - Kaatje Toye
- Department of Endocrinology and Unit for Osteoporosis and Metabolic Bone Diseases, Ghent University Hospital, 9000 Ghent, Belgium
| | - Viviane Van Hoof
- Department of Clinical Chemistry, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Ilse Luyckx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Hugo S A Heymans
- Department of Pediatrics, Emma's Children's Hospital - Academic Medical Centre, 1105 AZ Amsterdam, the Netherlands
| | - Eelco Dulfer
- Department of Medical Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Ian R Berry
- Leeds Genetics Laboratory, St James's University Hospital, Leeds LS7 4SA, UK
| | - Angus Dobbie
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds LS7 4SA, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Bart Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Eric A Espiner
- Department of Medicine, University of Otago, Christchurch 8011, New Zealand
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Peter Houpt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Isala Clinics, 8025 AB Zwolle, the Netherlands
| | - Geert R Mortier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium.
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13
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Green L, Berry IR, Childs AM, McCullagh H, Jose S, Warren D, Craven I, Camm N, Prescott K, van der Knaap MS, Sheridan E, Livingston JH. Whole Exon Deletion in the GFAP Gene Is a Novel Molecular Mechanism Causing Alexander Disease. Neuropediatrics 2018; 49:118-122. [PMID: 29253910 DOI: 10.1055/s-0037-1608921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Alexander disease (AD) is a leukodystrophy caused by heterozygous mutations in the gene encoding the glial fibrillary acidic protein (GFAP). Currently, de novo heterozygous missense mutations in the GFAP gene are identified in over 95% of patients with AD. However, patients with biopsy-proven AD have been reported in whom no GFAP mutation has been identified. We report identical twin boys presenting in infancy with seizures and developmental delay in whom MR appearances were suggestive of AD with the exception of an unusual, bilateral, arc of calcification at the frontal white-gray junction. Initial mutation screening of the GFAP gene did not identify a mutation. Whole exome sequencing in both brothers revealed a de novo heterozygous in-frame deletion of the whole of exon 5 of the GFAP gene. Mutations in the GFAP gene are thought to result in a toxic effect of mutant GFAP disrupting the formation of the normal intermediate filament network and resulting in Rosenthal fiber formation, which has hitherto not been linked to exonic scale copy number variants in GFAP. Further studies on mutation negative AD patients are warranted to determine whether a similar mechanism underlies their disease.
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Affiliation(s)
- Lydia Green
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Ian R Berry
- Leeds Genetics Laboratory, St. James's University Hospital, Leeds, United Kingdom
| | - Anne-Marie Childs
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Helen McCullagh
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | | | - Dan Warren
- Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Ian Craven
- Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Nick Camm
- Leeds Genetics Laboratory, St. James's University Hospital, Leeds, United Kingdom
| | | | - Marjo S van der Knaap
- Department of Child Neurology, VU University Medical Center, Amsterdam, The Netherlands
| | - Eamonn Sheridan
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
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14
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Jewell R, Brewer P, Stenton S, Berry IR, Chatfield S, Fernandes JA, Peres C, Wagner BE, Bennett C. Geroderma osteodysplasticum: Histological features and the role of panel-based exome sequencing in diagnosis. Ultrastruct Pathol 2018; 42:91-96. [PMID: 29424602 DOI: 10.1080/01913123.2018.1427166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Geroderma osteodysplasticum (GO) has clinical and histological features that overlap with other causes of wrinkly skin. Here we present the case of a child diagnosed with GO following exome sequencing of a panel of genes covering the wide differential diagnosis. The histological features of the overlapping conditions are presented, highlighting the utility of panel testing for conditions of this type. This is relevant to many genetic conditions and can influence ongoing management as exemplified by this case.
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Affiliation(s)
- Rosalyn Jewell
- a Yorkshire Regional Genetics Service , Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust , Leeds , UK
| | - Paul Brewer
- b Department of Orthopaedics , Sheffield Children's Hospital , Sheffield , UK
| | - Sophie Stenton
- c Department of Histopathology , Sheffield Teaching Hospitals , Sheffield , UK
| | - Ian R Berry
- d Leeds Genetics Laboratory , St James' Hospital, Leeds Teaching Hospitals NHS Trust , Leeds , UK
| | - Sue Chatfield
- e Women's and Newborn Unit, Bradford Royal Infirmary, Bradford Teaching Hospitals NHS Foundation Trust , Bradford , UK
| | - James A Fernandes
- b Department of Orthopaedics , Sheffield Children's Hospital , Sheffield , UK
| | - Cesar Peres
- c Department of Histopathology , Sheffield Teaching Hospitals , Sheffield , UK
| | - Bart E Wagner
- c Department of Histopathology , Sheffield Teaching Hospitals , Sheffield , UK
| | - Christopher Bennett
- a Yorkshire Regional Genetics Service , Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust , Leeds , UK
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15
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Singh RR, Livingston J, Lim M, Berry IR, Siddiqui A. An unusual neuroimaging finding and response to immunotherapy in a child with genetically confirmed vanishing white matter disease. Eur J Paediatr Neurol 2017; 21:410-413. [PMID: 27665184 DOI: 10.1016/j.ejpn.2016.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 05/11/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We present an unusual neuroimaging finding in a young girl with genetically confirmed vanishing white matter disease and a possible response to immunotherapy. METHODS AND RESULTS 2.5 yr old girl, presented with acute onset unsteadiness and encephalopathy following a viral illness. MRI showed global symmetric white matter abnormality, with symmetric enhancement of cranial nerves (III and V) and of cervical and lumbar roots. She received immunotherapy for her encephalopathic illness with white matter changes. Follow up neuroimaging showed resolution of white matter edema and resolution of the change in the brainstem. Genetic testing confirmed a diagnosis of vanishing white matter disease (VWMD). CONCLUSION Craniospinal nerve enhancement and possible response to immunotherapy has not been described in vanishing white matter disease.
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Affiliation(s)
- Rahul Raman Singh
- Department of Children's Neurosciences, Guys and St. Thomas' Hospital NHS Foundation Trust, Kings Health Partners, London, UK.
| | - John Livingston
- Department of Paediatric Neurology, Leeds General Infirmary, Leeds, UK.
| | - Ming Lim
- Department of Children's Neurosciences, Guys and St. Thomas' Hospital NHS Foundation Trust, Kings Health Partners, London, UK.
| | - Ian R Berry
- Leeds Genetics Laboratory, St. James's University Hospital, Leeds, UK.
| | - Ata Siddiqui
- Department of Neuroradiology, Guys and St. Thomas' Hospital NHS Foundation Trust, Kings Health Partners, London, UK.
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16
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Watson CM, Crinnion LA, Berry IR, Harrison SM, Lascelles C, Antanaviciute A, Charlton RS, Dobbie A, Carr IM, Bonthron DT. Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. BMC Med Genet 2016; 17:1. [PMID: 26729329 PMCID: PMC4700600 DOI: 10.1186/s12881-015-0265-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/16/2015] [Indexed: 12/16/2022]
Abstract
Background The widespread adoption of high-throughput sequencing technologies by genetic diagnostic laboratories has enabled significant expansion of their testing portfolios. Rare autosomal recessive conditions have been a particular focus of many new services. Here we report a cohort of 26 patients referred for genetic analysis of Joubert (JBTS) and Meckel-Gruber (MKS) syndromes, two clinically and genetically heterogeneous neurodevelopmental conditions that define a phenotypic spectrum, with MKS at the severe end. Methods Exome sequencing was performed for all cases, using Agilent SureSelect v5 reagents and Illumina paired-end sequencing. For two cases medium-coverage (9×) whole genome sequencing was subsequently undertaken. Results Using a standard analysis pipeline for the detection of single nucleotide and small insertion or deletion variants, molecular diagnoses were confirmed in 12 cases (4 %). Seeking to determine whether our cohort harboured pathogenic copy number variants (CNV), in JBTS- or MKS-associated genes, targeted comparative read-depth analysis was performed using FishingCNV. These analyses identified a putative intragenic AHI1 deletion that included three exons spanning at least 3.4 kb and an intergenic MPP4 to TMEM237 deletion that included exons spanning at least 21.5 kb. Whole genome sequencing enabled confirmation of the deletion-containing alleles and precise characterisation of the mutation breakpoints at nucleotide resolution. These data were validated following development of PCR-based assays that could be subsequently used for “cascade” screening and/or prenatal diagnosis. Conclusions Our investigations expand the AHI1 and TMEM237 mutation spectrum and highlight the importance of performing CNV screening of disease-associated genes. We demonstrate a robust increasingly cost-effective CNV detection workflow that is applicable to all MKS/JBTS referrals. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0265-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ian R Berry
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Sally M Harrison
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Carolina Lascelles
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Agne Antanaviciute
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ruth S Charlton
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Angus Dobbie
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ian M Carr
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
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17
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Chan AOK, But WM, Ng KL, Wong LM, Lam YY, Tiu SC, Lee KF, Lee CY, Loung PY, Berry IR, Brown R, Charlton R, Cheng CW, Ho YC, Tse WY, Shek CC. Molecular analysis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency in Hong Kong Chinese patients. Steroids 2011; 76:1057-62. [PMID: 21570420 DOI: 10.1016/j.steroids.2011.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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] [Received: 01/20/2011] [Revised: 04/18/2011] [Accepted: 04/20/2011] [Indexed: 11/16/2022]
Abstract
BACKGROUND Congenital adrenal hyperplasia (CAH) caused by 21-hydroxylase deficiency (21OHD) is an autosomal recessive disorder due to mutation in the CYP21A2 gene. OBJECTIVE To elucidate the genetic basis of 21-hydroxylase-deficient CAH in Hong Kong Chinese patients. PATIENTS AND METHODS Mutational analysis of the CYP21A2 gene was performed on 35 Hong Kong Chinese patients with 21OHD using direct DNA sequencing and multiplex ligation-dependent probe amplification (MLPA). RESULTS The genetic findings of 21 male and 14 female patients are the following: c.293-13A/C>G (intron 2 splice site; 20 alleles), p.I172N (13), p.R356W (7), p.Q318X (4). A total of 20 mutant alleles contained gross deletion/conversion of all or part of the CYP21A2 gene. A novel mutation, c.1367delA (p.D456fs), was detected in one patient. One patient had only a heterozygous mutation detected. Out of 35 patients, 16 would have been incorrectly genotyped if either DNA sequencing or MLPA alone was used for molecular analysis. CONCLUSIONS The frequency of various mutations in the studied patients differs from those reported in other Asian populations. Gross deletion/conversion accounts for nearly one-third of the genetic defects. Therefore, laboratories must include methods for detecting point mutations as well as gross deletions/conversions to avoid misinterpretation of genotype. Genotyping has increasingly been proven to be a useful tool for supplementing, if not replacing, hormonal profiling for the diagnosis of 21OHD.
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Affiliation(s)
- Angel O K Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong.
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