1
|
Tenorio RB, Camargo CHF, Donis KC, Almeida CCB, Teive HAG. Diagnostic Yield of NGS Tests for Hereditary Ataxia: a Systematic Review. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1552-1565. [PMID: 37950147 DOI: 10.1007/s12311-023-01629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS), comprising targeted panels (TP), exome sequencing (ES), and genome sequencing (GS) became robust clinical tools for diagnosing hereditary ataxia (HA). Determining their diagnostic yield (DY) is crucial for optimal clinical decision-making. We conducted a comprehensive systematic literature review on the DY of NGS tests for HA. We searched PubMed and Embase databases for relevant studies between 2016 and 2022 and manually examined reference lists of relevant reviews. Eligible studies described the DY of NGS tests in patients with ataxia as a significant feature. Data from 33 eligible studies showed a median DY of 43% (IQR = 9.5-100%). The median DY for TP and ES was 46% and 41.9%, respectively. Higher DY was associated with specific phenotype selection, such as episodic ataxia at 68.35% and early and late onset of ataxia at 46.4% and 54.4%. Parental consanguinity had a DY of 52.4% (p = 0.009), and the presumed autosomal recessive (AR) inheritance pattern showed 62.5%. There was a difference between the median DY of studies that performed targeted sequencing (tandem repeat expansion, TRE) screening and those that did not (p = 0.047). A weak inverse correlation was found between DY and the extent of previous genetic investigation (rho = - 0.323; p = 0.065). The most common genes were CACNA1A and SACS. DY was higher for presumed AR inheritance pattern, positive family history, and parental consanguinity. ES appears more advantageous due to the inclusion of rare genes that might be excluded in TP.
Collapse
Affiliation(s)
- Renata Barreto Tenorio
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.
| | - Carlos Henrique F Camargo
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Hélio A G Teive
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
| |
Collapse
|
2
|
Felício D, Santos M. Spinocerebellar ataxia type 11 (SCA11): TTBK2 variants, functions and associated disease mechanisms. CEREBELLUM (LONDON, ENGLAND) 2024; 23:678-687. [PMID: 36892783 PMCID: PMC10951003 DOI: 10.1007/s12311-023-01540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/10/2023]
Abstract
Spinocerebellar ataxia type 11 (SCA11) is a rare type of autosomal dominant cerebellar ataxia, mainly characterized by progressive cerebellar ataxia, abnormal eye signs and dysarthria. SCA11 is caused by variants in TTBK2, which encodes tau tubulin kinase 2 (TTBK2) protein. Only a few families with SCA11 were described to date, all harbouring small deletions or insertions that result in frameshifts and truncated TTBK2 proteins. In addition, TTBK2 missense variants were also reported but they were either benign or still needed functional validation to ascertain their pathogenic potential in SCA11. The mechanisms behind cerebellar neurodegeneration mediated by TTBK2 pathogenic alleles are not clearly established. There is only one neuropathological report and a few functional studies in cell or animal models published to date. Moreover, it is still unclear whether the disease is caused by TTBK2 haploinsufficiency of by a dominant negative effect of TTBK2 truncated forms on the normal allele. Some studies point to a lack of kinase activity and mislocalization of mutated TTBK2, while others reported a disruption of normal TTBK2 function caused by SCA11 alleles, particularly during ciliogenesis. Although TTBK2 has a proven function in cilia formation, the phenotype caused by heterozygous TTBK2 truncating variants are not clearly typical of ciliopathies. Thus, other cellular mechanisms may explain the phenotype seen in SCA11. Neurotoxicity caused by impaired TTBK2 kinase activity against known neuronal targets, such as tau, TDP-43, neurotransmitter receptors or transporters, may contribute to neurodegeneration in SCA11.
Collapse
Affiliation(s)
- Daniela Felício
- UnIGENe, IBMC-Institute for Molecular and Cell Biology, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313, Porto, Portugal
| | - Mariana Santos
- UnIGENe, IBMC-Institute for Molecular and Cell Biology, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
| |
Collapse
|
3
|
Neagu AC, Budișteanu M, Gheorghe DC, Mocanu AI, Mocanu H. Rare Gene Mutations in Romanian Hypoacusis Patients: Case Series and a Review of the Literature. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58091252. [PMID: 36143929 PMCID: PMC9501263 DOI: 10.3390/medicina58091252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
(1) Background: In this paper, we report on three cases of hypoacusis as part of a complex phenotype and some rare gene variants. An extensive review of literature completes the newly reported clinical and genetic information. (2) Methods: The cases range from 2- to 11-year-old boys, all with a complex clinical picture and hearing impairment. In all cases, whole exome sequencing (WES) was performed, in the first case in association with mitochondrial DNA study. (3) Results: The detected variants were: two heterozygous variants in the TWNK gene, one likely pathogenic and another of uncertain clinical significance (autosomal recessive mitochondrial DNA depletion syndrome type 7-hepatocerebral type); heterozygous variants of uncertain significance PACS2 and SYT2 genes (autosomal dominant early infantile epileptic encephalopathy) and a homozygous variant of uncertain significance in SUCLG1 gene (mitochondrial DNA depletion syndrome 9). Some of these genes have never been previously reported as associated with hearing problems. (4) Conclusions: Our cases bring new insights into some rare genetic syndromes. Although the role of TWNK gene in hearing impairment is clear and accordingly reflected in published literature as well as in the present article, for the presented gene variants, a correlation to hearing problems could not yet be established and requires more scientific data. We consider that further studies are necessary for a better understanding of the role of these variants.
Collapse
Affiliation(s)
- Alexandra-Cristina Neagu
- Department of ENT&HNS, “Marie Sklodowska Curie” Emergency Children’s Hospital, 041434 Bucharest, Romania
| | - Magdalena Budișteanu
- Department of Medical Genetics, Faculty of Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
- Correspondence: (M.B.); (A.-I.M.); Tel.: +407-2292-9091 (M.B.); +407-2340-0435 (A.-I.M.)
| | - Dan-Cristian Gheorghe
- Department of ENT&HNS, “Marie Sklodowska Curie” Emergency Children’s Hospital, 041434 Bucharest, Romania
- Department of ENT&HNS, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Adela-Ioana Mocanu
- Department of ENT&HNS, Polimed Medical Center, 040067 Bucharest, Romania
- Correspondence: (M.B.); (A.-I.M.); Tel.: +407-2292-9091 (M.B.); +407-2340-0435 (A.-I.M.)
| | - Horia Mocanu
- Department of ENT&HNS, Faculty of Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
| |
Collapse
|
4
|
Botte M, Huber S, Bucher D, Klint JK, Rodríguez D, Tagmose L, Chami M, Cheng R, Hennig M, Abdul Rahman W. Apo and ligand-bound high resolution Cryo-EM structures of the human Kv3.1 channel reveal a novel binding site for positive modulators. PNAS NEXUS 2022; 1:pgac083. [PMID: 36741467 PMCID: PMC9896932 DOI: 10.1093/pnasnexus/pgac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023]
Abstract
Kv3 ion-channels constitute a class of functionally distinct voltage-gated ion channels characterized by their ability to fire at a high frequency. Several disease relevant mutants, together with biological data, suggest the importance of this class of ion channels as drug targets for CNS disorders, and several drug discovery efforts have been reported. Despite the increasing interest for this class of ion channels, no structure of a Kv3 channel has been reported yet. We have determined the cryo-EM structure of Kv3.1 at 2.6 Å resolution using full-length wild type protein. When compared to known structures for potassium channels from other classes, a novel domain organization is observed with the cytoplasmic T1 domain, containing a well-resolved Zinc site and displaying a rotation by 35°. This suggests a distinct cytoplasmic regulation mechanism for the Kv3.1 channel. A high resolution structure was obtained for Kv3.1 in complex with a novel positive modulator Lu AG00563. The structure reveals a novel ligand binding site for the Kv class of ion channels located between the voltage sensory domain and the channel pore, a region which constitutes a hotspot for disease causing mutations. The discovery of a novel binding site for a positive modulator of a voltage-gated potassium channel could shed light on the mechanism of action for these small molecule potentiators. This finding could enable structure-based drug design on these targets with high therapeutic potential for the treatment of multiple CNS disorders.
Collapse
Affiliation(s)
- Mathieu Botte
- leadXpro AG, PARK InnovAARE, 5234 Villigen, Switzerland
| | - Sophie Huber
- leadXpro AG, PARK InnovAARE, 5234 Villigen, Switzerland
| | - Denis Bucher
- leadXpro AG, PARK InnovAARE, 5234 Villigen, Switzerland
| | | | | | - Lena Tagmose
- H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Mohamed Chami
- BioEM laboratory, Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Robert Cheng
- leadXpro AG, PARK InnovAARE, 5234 Villigen, Switzerland
| | | | | |
Collapse
|
5
|
Subramony SH, Burns M, Kugelmann EL, Zingariello CD. Inherited Ataxias in Children. Pediatr Neurol 2022; 131:54-62. [PMID: 35490578 DOI: 10.1016/j.pediatrneurol.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
The purpose of this review is to describe the current diagnostic approach to inherited ataxias during childhood. With the expanding use and availability of gene testing technologies including large sequencing panels, the ability to arrive at a precise genetic diagnosis in this group of disorders has been improving. We have reviewed all the gene sequencing studies of ataxias available by a comprehensive literature search and summarize their results. We provide a logical algorithm for a diagnostic approach in the context of this evolving information. We stress the fact that both autosomal recessive and autosomal dominant mutations can occur in children with ataxias and the need for keeping in mind nucleotide repeat expansions, which cannot be detected by sequencing technologies, as a possible cause of progressive ataxias in children. We discuss the traditional phenotype-based diagnostic approach in the context of gene testing technologies. Finally, we summarize those disorders in which a specific therapy may be indicated.
Collapse
Affiliation(s)
- Sub H Subramony
- Department of Neurology, University of Florida College of Medicine, Gainesville, Florida; Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida.
| | - Matthew Burns
- Department of Neurology, University of Florida College of Medicine, Gainesville, Florida
| | - E Lee Kugelmann
- Department of Neurology, University of Florida College of Medicine, Gainesville, Florida
| | - Carla D Zingariello
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida
| |
Collapse
|
6
|
Application of a custom NGS gene panel revealed a high diagnostic utility for molecular testing of hereditary ataxias. J Appl Genet 2022; 63:513-525. [PMID: 35588347 DOI: 10.1007/s13353-022-00701-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/05/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022]
Abstract
Hereditary ataxias (HA) are a rare group of heterogeneous disorders. Here, we present the results of molecular testing of a group of ataxia patients using a custom-designed next-generation sequencing (NGS) panel. Due to the genetic and clinical overlapping of hereditary ataxias and spastic paraplegias (HSP), the panel encompasses together HA and HSP genes. The NGS libraries, comprising coding sequences for 152 genes, were performed using KAPA HyperPlus and HyperCap Target Enrichment Kit, sequenced on the MiSeq instrument. The results were analyzed using the BaseSpace Variant Interpreter and Integrative Genomics Viewer. All pathogenic and likely pathogenic variants were confirmed using Sanger sequencing. A total of 29 patients with hereditary ataxias were enrolled in the NGS testing, and 16 patients had a confirmed molecular diagnosis with diagnostic accuracy rate of 55.2%. Pathogenic or likely pathogenic mutations were identified in 10 different genes: POLG (PEOA1, n = 3; SCAE, n = 2), CACNA1A (EA2, n = 2), SACS (ARSACS, n = 2), SLC33A1 (SPG42, n = 2), STUB1 (SCA48, n = 1), SPTBN2 (SCA5, n = 1), TGM6 (SCA35, n = 1), SETX (AOA2, n = 1), ANO10 (SCAR10, n = 1), and SPAST (SPG4, n = 1). We demonstrated that an approach based on the targeted use of the NGS panel can be highly effective and a useful tool in the molecular diagnosis of ataxia patients. Furthermore, we highlight the fact that a sequencing panel targeting both ataxias and HSP genes increases the diagnostic success level.
Collapse
|
7
|
Ghorbani F, Alimohamed MZ, Vilacha JF, Van Dijk KK, De Boer-Bergsma J, Fokkens MR, Lemmink H, Sijmons RH, Sikkema-Raddatz B, Groves MR, Verschuuren-Bemelmans CC, Verbeek DS, Van Diemen CC, Westers H. Feasibility of Follow-Up Studies and Reclassification in Spinocerebellar Ataxia Gene Variants of Unknown Significance. Front Genet 2022; 13:782685. [PMID: 35401678 PMCID: PMC8990126 DOI: 10.3389/fgene.2022.782685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Genetic testing for SCA leads to diagnosis, prognosis and risk assessment for patients and their family members. While advances in sequencing and computing technologies have provided researchers with a rapid expansion in the genetic test content that can be used to unravel the genetic causes that underlie diseases, the large number of variants with unknown significance (VUSes) detected represent challenges. To minimize the proportion of VUSes, follow-up studies are needed to aid in their reclassification as either (likely) pathogenic or (likely) benign variants. In this study, we addressed the challenge of prioritizing VUSes for follow-up using (a combination of) variant segregation studies, 3D protein modeling, in vitro splicing assays and functional assays. Of the 39 VUSes prioritized for further analysis, 13 were eligible for follow up. We were able to reclassify 4 of these VUSes to LP, increasing the molecular diagnostic yield by 1.1%. Reclassification of VUSes remains difficult due to limited possibilities for performing variant segregation studies in the classification process and the limited availability of routine functional tests.
Collapse
Affiliation(s)
- Fatemeh Ghorbani
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mohamed Z. Alimohamed
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Shree Hindu Mandal Hospital, Dar es Salaam, Tanzania
| | - Juliana F. Vilacha
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Krista K. Van Dijk
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jelkje De Boer-Bergsma
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Michiel R. Fokkens
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Rolf H. Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Matthew R. Groves
- Structural Biology in Drug Design, Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | | | - Dineke S. Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- *Correspondence: Dineke S. Verbeek,
| | - Cleo C. Van Diemen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Helga Westers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| |
Collapse
|
8
|
Rajan DS, Kour S, Fortuna TR, Cousin MA, Barnett SS, Niu Z, Babovic-Vuksanovic D, Klee EW, Kirmse B, Innes M, Rydning SL, Selmer KK, Vigeland MD, Erichsen AK, Nemeth AH, Millan F, DeVile C, Fawcett K, Legendre A, Sims D, Schnekenberg RP, Burglen L, Mercier S, Bakhtiari S, Francisco-Velilla R, Embarc-Buh A, Martinez-Salas E, Wigby K, Lenberg J, Friedman JR, Kruer MC, Pandey UB. Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5. Front Cell Dev Biol 2022; 10:783762. [PMID: 35295849 PMCID: PMC8918504 DOI: 10.3389/fcell.2022.783762] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/17/2022] [Indexed: 01/01/2023] Open
Abstract
The hereditary ataxias are a heterogenous group of disorders with an increasing number of causative genes being described. Due to the clinical and genetic heterogeneity seen in these conditions, the majority of such individuals endure a diagnostic odyssey or remain undiagnosed. Defining the molecular etiology can bring insights into the responsible molecular pathways and eventually the identification of therapeutic targets. Here, we describe the identification of biallelic variants in the GEMIN5 gene among seven unrelated families with nine affected individuals presenting with spastic ataxia and cerebellar atrophy. GEMIN5, an RNA-binding protein, has been shown to regulate transcription and translation machinery. GEMIN5 is a component of small nuclear ribonucleoprotein (snRNP) complexes and helps in the assembly of the spliceosome complexes. We found that biallelic GEMIN5 variants cause structural abnormalities in the encoded protein and reduce expression of snRNP complex proteins in patient cells compared with unaffected controls. Finally, knocking out endogenous Gemin5 in mice caused early embryonic lethality, suggesting that Gemin5 expression is crucial for normal development. Our work further expands on the phenotypic spectrum associated with GEMIN5-related disease and implicates the role of GEMIN5 among patients with spastic ataxia, cerebellar atrophy, and motor predominant developmental delay.
Collapse
Affiliation(s)
- Deepa S. Rajan
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Sukhleen Kour
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tyler R. Fortuna
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Margot A. Cousin
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Sarah S. Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Dusica Babovic-Vuksanovic
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Eric W. Klee
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Brian Kirmse
- Division of Genetics, University of Mississippi Medical Center, Jackson, MS, United States
| | - Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Kaja K. Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Magnus Dehli Vigeland
- Department of Medical Genetics, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Andrea H. Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Katherine Fawcett
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Adrien Legendre
- Laboratoire de biologie médicale multisites Seqoia—FMG2025, Paris, France
| | - David Sims
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet et Laboratoire de Neurogénétique Moléculaire, Département de Génétique, AP-HP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Nantes, France
- Nantes Université, CNRS, INSERM, l’institut du thorax, Nantes, France
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | | | - Azman Embarc-Buh
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | - Kristen Wigby
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jerica Lenberg
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jennifer R. Friedman
- Department of Neurosciences, University of California San Diego, San Diego, CA, United States
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Michael C. Kruer
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- *Correspondence: Udai Bhan Pandey,
| |
Collapse
|
9
|
A Novel SETX Mutation in a Taiwanese Patient with Autosomal Recessive Cerebellar Ataxia Detected by Targeted Next-Generation Sequencing, and a Literature Review. Brain Sci 2022; 12:brainsci12020173. [PMID: 35203940 PMCID: PMC8869917 DOI: 10.3390/brainsci12020173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Ataxia with oculomotor apraxia type 2 (AOA2), also known as autosomal recessive spinocerebellar ataxia with axonal neuropathy-2 (SCAN2) (OMIM #606002), is a neurodegenerative disorder characterized by early-onset progressive cerebellar ataxia, polyneuropathy, and elevated levels of alpha-fetoprotein. It is caused by mutations in the SETX (OMIM #608465) gene. The prevalence of this disease is widely varied, from non-existent up to 1/150,000, depending on the region. Until now, no cases of AOA2/SCAN2 have been reported in Taiwan. Methods: Next-generation sequencing was used to detect disease-causing mutations of SETX in a Taiwanese patient presenting with autosomal recessive cerebellar ataxia, polyneuropathy, and elevated alpha-fetoprotein. The candidate mutations were further confirmed by polymerase chain reaction (PCR) and Sanger sequencing. Results: A compound heterozygous mutation of SETX c.6859C > T (p.R2287X) and c.7034-7036del was identified. The c.6859C > T (p.R2287X) has been previously found in a Saudi Arabia family, whereas c.7034-7036del is a novel mutation. Both mutations were predicted by bioinformatics programs to be likely pathogenic (having a damaging effect). We also reviewed the literature to address the reported clinical features of AOA2 from different populations. Conclusions: To our knowledge, we are the first to report a Taiwanese patient with AOA2/SCAN2, a result obtained by utilizing next-generation sequencing. The literature review shows that ataxia, polyneuropathy, and elevated AFP are common features and ocular motor apraxia (OMA) is a variable sign of AOA2 from different populations. OMA is rare and saccadic ocular pursuit and nystagmus are common in East Asian AOA2.
Collapse
|
10
|
Tang Y, Zhao D, Wang S, Yi Q, Xia Y, Geng B. Diagnostic Value of Next-Generation Sequencing in Periprosthetic Joint Infection: A Systematic Review. Orthop Surg 2021; 14:190-198. [PMID: 34935279 PMCID: PMC8867422 DOI: 10.1111/os.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023] Open
Abstract
Next‐generation sequencing (NGS) has developed rapidly in the last decade and is emerging as a promising diagnostic tool for periprosthetic joint infection (PJI). However, its diagnostic value for PJI is still uncertain. This systematic review aimed to explore the diagnostic value of NGS for PJI and verify its accuracy for culture‐negative PJI patients. We conducted this systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) guidelines. Medline, Embase, and Cochrane Library were searched to identify diagnostic technique studies evaluating the accuracy of NGS in the diagnosis of PJI. The diagnostic sensitivity, specificity, and positive and negative predictive values were estimated for each article. The detection rate of NGS for culture‐negative PJI patients or PJI patients with antibiotic administration history was also calculated. Of the 87 identified citations, nine studies met the inclusion criteria. The diagnostic sensitivities and specificities of NGS ranged from 63% to 96% and 73% to 100%, respectively. The positive and negative predictive values ranged from 71% to 100% and 74% to 95%, respectively. The detection rate of NGS for culture‐negative PJI patients in six studies was higher than 50% (range from 82% to 100%), while in three studies it was lower than 50% (range from 9% to 31%). Also, the detection rate of NGS for PJIs with antibiotic administration history ranged from 74.05% to 92.31%. In conclusion, this systematic review suggests that NGS may have the potential to be a new tool for the diagnosis of PJI and should be considered to be added to the portfolio of diagnostic procedures. Furthermore, NGS showed a favorable diagnostic accuracy for culture‐negative PJI patients or PJI patients with antibiotic administration history. However, due to the small sample sizes of studies and substantial heterogeneity among the included studies, more research is needed to confirm or disprove these findings.
Collapse
Affiliation(s)
- Yuchen Tang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Dacheng Zhao
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Shenghong Wang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Qiong Yi
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yayi Xia
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Bin Geng
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| |
Collapse
|
11
|
Zhang Y, Quraishi IH, McClure H, Williams LA, Cheng Y, Kale S, Dempsey GT, Agrawal S, Gerber DJ, McManus OB, Kaczmarek LK. Suppression of Kv3.3 channels by antisense oligonucleotides reverses biochemical effects and motor impairment in spinocerebellar ataxia type 13 mice. FASEB J 2021; 35:e22053. [PMID: 34820911 DOI: 10.1096/fj.202101356r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/26/2021] [Accepted: 11/08/2021] [Indexed: 11/11/2022]
Abstract
Mutations in KCNC3, the gene that encodes the Kv3.3 voltage dependent potassium channel, cause Spinocerebellar Ataxia type 13 (SCA13), a disease associated with disrupted motor behaviors, progressive cerebellar degeneration, and abnormal auditory processing. The Kv3.3 channel directly binds Hax-1, a cell survival protein. A disease-causing mutation, Kv3.3-G592R, causes overstimulation of Tank Binding Kinase 1 (Tbk1) in the cerebellum, resulting in the degradation of Hax-1 by promoting its trafficking into multivesicular bodies and then to lysosomes. We have now tested the effects of antisense oligonucleotides (ASOs) directed against the Kv3.3 channel on both wild type mice and those bearing the Kv3.3-G592R-encoding mutation. Intracerebroventricular infusion of the Kcnc3-specific ASO suppressed both mRNA and protein levels of the Kv3.3 channel. In wild-type animals, this produced no change in levels of activated Tbk1, Hax-1 or Cd63, a tetraspanin marker for late endosomes/multivesicular bodies. In contrast, in mice homozygous for the Kv3.3-G592R-encoding mutation, the same ASO reduced Tbk1 activation and levels of Cd63, while restoring the expression of Hax-1 in the cerebellum. The motor behavior of the mice was tested using a rotarod assay. Surprisingly, the active ASO had no effects on the motor behavior of wild type mice but restored the behavior of the mutant mice to those of age-matched wild type animals. Our findings indicate that, in mature intact animals, suppression of Kv3.3 expression can reverse the deleterious effects of a SCA13 mutation while having little effect on wild type animals. Thus, targeting Kv3.3 expression may prove a viable therapeutic approach for SCA13.
Collapse
Affiliation(s)
- Yalan Zhang
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Imran H Quraishi
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Heather McClure
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | | | | | | | | | | | | - Leonard K Kaczmarek
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
12
|
Abstract
Leukodystrophies are a group of genetically determined disorders that affect development or maintenance of central nervous system myelin. Leukodystrophies have an incidence of at least 1 in 4700 live births and significant morbidity and elevated risk of early death. This report includes a discussion of the types of leukodystrophies; their prevalence, clinical presentation, symptoms, and diagnosis; and current and future treatments. Leukodystrophies can present at any age from infancy to adulthood, with variability in disease progression and clinical presentation, ranging from developmental delay to seizures to spasticity. Diagnosis is based on a combination of history, examination, and radiologic and laboratory findings, including genetic testing. Although there are few cures, there are significant opportunities for care and improvements in patient well-being. Rapid advances in imaging and diagnosis, the emergence of and requirement for timely treatments, and the addition of leukodystrophy screening to newborn screening, make an understanding of the leukodystrophies necessary for pediatricians and other care providers for children.
Collapse
Affiliation(s)
- Joshua L Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, University of Utah and Brain and Spine Center, Primary Children's Hospital, Salt Lake City, Utah
| | | | | |
Collapse
|
13
|
Pauly MG, Hellenbroich Y, Grundmann-Hauser K, Hinrichs F, Lohmann K, Brüggemann N. Compound Heterozygous DARS2 Mutations as a Mimic of Hereditary Spastic Paraplegia. Mov Disord Clin Pract 2021; 8:972-976. [PMID: 34405109 DOI: 10.1002/mdc3.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Martje G Pauly
- Institute of Neurogenetics University of Lübeck Lübeck Germany.,Institute of Systems Motor Science University of Lübeck Lübeck Germany.,Department of Neurology University Hospital Schleswig Holstein Lübeck Germany
| | | | - Kathrin Grundmann-Hauser
- Institute of Medical Genetics and Applied Genomics University Hospital of Tübingen Tübingen Germany
| | - Frauke Hinrichs
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Katja Lohmann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics University of Lübeck Lübeck Germany.,Department of Neurology University Hospital Schleswig Holstein Lübeck Germany.,Center for Brain, Behavior and Metabolism University of Lübeck Lübeck Germany
| |
Collapse
|
14
|
NGS in Hereditary Ataxia: When Rare Becomes Frequent. Int J Mol Sci 2021; 22:ijms22168490. [PMID: 34445196 PMCID: PMC8395181 DOI: 10.3390/ijms22168490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/17/2022] Open
Abstract
The term hereditary ataxia (HA) refers to a heterogeneous group of neurological disorders with multiple genetic etiologies and a wide spectrum of ataxia-dominated phenotypes. Massive gene analysis in next-generation sequencing has entered the HA scenario, broadening our genetic and clinical knowledge of these conditions. In this study, we employed a targeted resequencing panel (TRP) in a large and highly heterogeneous cohort of 377 patients with a clinical diagnosis of HA, but no molecular diagnosis on routine genetic tests. We obtained a positive result (genetic diagnosis) in 33.2% of the patients, a rate significantly higher than those reported in similar studies employing TRP (average 19.4%), and in line with those performed using exome sequencing (ES, average 34.6%). Moreover, 15.6% of the patients had an uncertain molecular diagnosis. STUB1, PRKCG, and SPG7 were the most common causative genes. A comparison with published literature data showed that our panel would have identified 97% of the positive cases reported in previous TRP-based studies and 92% of those diagnosed by ES. Proper use of multigene panels, when combined with detailed phenotypic data, seems to be even more efficient than ES in clinical practice.
Collapse
|
15
|
Wan N, Chen Z, Wan L, Yuan H, Tang Z, Liu M, Peng Y, Peng L, Lei L, Xie Y, Deng Q, Wang S, Wang C, Peng H, Hou X, Shi Y, Long Z, Qiu R, Xia K, Tang B, Jiang H. Genetic etiology of a Chinese ataxia cohort: Expanding the mutational spectrum of hereditary ataxias. Parkinsonism Relat Disord 2021; 89:120-127. [PMID: 34284285 DOI: 10.1016/j.parkreldis.2021.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Hereditary ataxias demonstrate a high degree of clinical and genetic heterogeneity. Understanding the genetic etiology of hereditary ataxias is crucial for genetic counseling and clinical management. METHODS The clinical and genetic data of patients with familial or sporadic ataxias who referred to our tertiary medical center were retrospectively analyzed. Probands in this study underwent SCA repeat expansion panel firstly to screen for repeat expansion SCAs; those with negative results had NGS-targeted panels or WES testing to detect conventional mutations. RESULTS A total of 223 patients were enrolled from 206 families. 5 kinds of coexisting SCA repeat expansions were observed (SCA3/SCA17, SCA3/SCA8, SCA2/SCA8, SCA3/SCA12 and SCA8/SCA12) in 12 patients from 8 families, among which SCA2/SCA8, SCA8/SCA12 and SCA3/SCA12 were reported for the first time. The coexistence of expanded SCA3 with SCA17 alleles was the most common in our study. NGS identified pathogenic/likely pathogenic variants in 12 ataxia causative genes in 13 probands. Spastic paraplegia ataxia was the most common diagnosis. Six novel mutations were detected in five ataxia-related genes. CONCLUSION Coexistence may not specific to a certain SCA subtype and the frequency might have been underestimated before. SCA repeat expansion panel should be considered in patients with overlapping SCA features. In addition, our study broadened the conventional mutation spectrum in ataxia-related genes. These results facilitate a better understanding of the genetic basis for hereditary ataxias.
Collapse
Affiliation(s)
- Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Linliu Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lijing Lei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yue Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qi Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Shang Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Huirong Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xuan Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Laboratory of Medical Genetics, Central South University, Changsha, China; School of Basic Medical Science, Central South University, Changsha, China.
| |
Collapse
|
16
|
Krygier M, Mazurkiewicz-Bełdzińska M. Milestones in genetics of cerebellar ataxias. Neurogenetics 2021; 22:225-234. [PMID: 34224032 PMCID: PMC8426223 DOI: 10.1007/s10048-021-00656-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/23/2021] [Indexed: 11/29/2022]
Abstract
Cerebellar ataxias (CAs) comprise a group of rare, neurological disorders characterized by extensive phenotypic and genetic heterogeneity. The core clinical feature is the cerebellar syndrome, which is often accompanied by other neurological or non-neurological signs. In the last 30 years, our understanding of the CA etiology has increased significantly, and numerous ataxia-associated genes have been discovered. Conventional variants or tandem repeat expansions, localized in the coding or non-coding DNA sequences, lead to hereditary ataxia, which can display different patterns of inheritance. Advances in molecular techniques have enabled a rapid and cost-effective detection of causative variants in a significant number of CA patients. However, despite performing extensive investigations, a definite diagnosis is still unknown in the majority of affected individuals. In this review, we discuss the major advances in the genetics of CAs over the last 30 years, focusing on the impact of next-generation sequencing on the genetic landscape of childhood- and adult-onset CAs. Additionally, we outline possible directions for further genetic research in hereditary and sporadic CAs in the era of increasing application of whole-genome sequencing and genome-wide association studies in various neurological disorders.
Collapse
Affiliation(s)
- Magdalena Krygier
- Department of Developmental Neurology, Medical University of Gdańsk, ul. Dębinki 7 80-952, Gdańsk, Poland.
| | | |
Collapse
|
17
|
Moraes MPMD, Rosa ABR, Jaques CS, Marussi VHR, Pedroso JL, Barsottini OG. X-linked adrenoleukodystrophy presenting as progressive ataxia and pure cerebellar involvement. ARQUIVOS DE NEURO-PSIQUIATRIA 2021; 79:463-464. [PMID: 34161534 DOI: 10.1590/0004-282x-anp-2020-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/19/2020] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Cristina Saade Jaques
- Universidade Federal de São Paulo, Unidade de Ataxia, Departamento de Neurologia, São Paulo SP, Brazil
| | - Victor Hugo Rocha Marussi
- Hospital Beneficência Portuguesa de São Paulo, Departamento de Neurorradiologia, São Paulo SP, Brazil.,Universidade Federal de São Paulo, Departamento de Radiologia, Divisão de Neurorradiologia, São Paulo SP, Brazil
| | - José Luiz Pedroso
- Universidade Federal de São Paulo, Unidade de Ataxia, Departamento de Neurologia, São Paulo SP, Brazil
| | | |
Collapse
|
18
|
da Graça FF, Peluzzo TM, Bonadia LC, Martinez ARM, Diniz de Lima F, Pedroso JL, Barsottini OGP, Gama MTD, Akçimen F, Dion PA, Rouleau GA, Marques W, França MC. Diagnostic Yield of Whole Exome Sequencing for Adults with Ataxia: a Brazilian Perspective. THE CEREBELLUM 2021; 21:49-54. [PMID: 33956305 DOI: 10.1007/s12311-021-01268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 12/14/2022]
Abstract
Previous studies using whole exome sequencing (WES) have shown that a significant proportion of adult patients with undiagnosed ataxia in European and North American cohorts have a known genetic cause. Little is known about the diagnostic yield of WES in non-Caucasian ataxic populations. Herein, we used WES to investigate a Brazilian cohort of 76 adult patients with idiopathic ataxia previously screened for trinucleotide expansions in known ataxia genes. We collected clinical and radiological data from each patient. WES was performed following standard procedures. Only variants labeled as pathogenic or likely pathogenic according to American college of medical genetics and genomics (ACMG) criteria were retrieved. We determined the diagnostic yield of WES for the whole cohort and also for subgroups defined according to presence or not of pyramidal signs, peripheral neuropathy, and cerebellar atrophy. There were 41 women and 35 men. Mean age at testing was 48 years. Pyramidal signs, peripheral neuropathy, tremor, and cerebellar atrophy were found in 38.1%, 13.1%, 10.5%, and 68.3% of all subjects, respectively. Diagnostic yield of WES was 35.5%. Thirty-six distinct mutations were found in 20 different genes, determining the diagnosis of 18 autosomal recessive and 9 autosomal dominant ataxias. SACS and SPG7 were the most frequently found underlying genes. WES performed better in the subgroup with vs the subgroup without spasticity (p = 0.005). WES was diagnostic in 35.5% of cases of the Brazilian cohort of ataxia cases. These results have implications for diagnosis, genetic counseling and eventually treatment.
Collapse
Affiliation(s)
- Felipe Franco da Graça
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - Thiago M Peluzzo
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Luciana Cardoso Bonadia
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Alberto Rolim Muro Martinez
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - Fabricio Diniz de Lima
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - José Luiz Pedroso
- Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Orlando G P Barsottini
- Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | | | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Wilson Marques
- Department of Neuroscience and Behavioural Science, School of Medicine, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Marcondes Cavalcante França
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.
| |
Collapse
|
19
|
Application of a Clinical Workflow May Lead to Increased Diagnostic Precision in Hereditary Spastic Paraplegias and Cerebellar Ataxias: A Single Center Experience. Brain Sci 2021; 11:brainsci11020246. [PMID: 33669240 PMCID: PMC7919782 DOI: 10.3390/brainsci11020246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 11/17/2022] Open
Abstract
The molecular characterization of Hereditary Spastic Paraplegias (HSP) and inherited cerebellar ataxias (CA) is challenged by their clinical and molecular heterogeneity. The recent application of Next Generation Sequencing (NGS) technologies is increasing the diagnostic rate, which can be influenced by patients’ selection. To assess if a clinical diagnosis of CA/HSP received in a third-level reference center might impact the molecular diagnostic yield, we retrospectively evaluated the molecular diagnostic rate reached in our center on 192 unrelated families (90 HSP and 102 CA) (i) before NGS and (ii) with the use of NGS gene panels. Overall, 46.3% of families received a genetic diagnosis by first-tier individual gene screening: 43.3% HSP and 50% spinocerebellar ataxias (SCA). The diagnostic rate was 56.7% in AD-HSP, 55.5% in AR-HSP, and 21.2% in sporadic HSP. On the other hand, 75% AD-, 52% AR- and 33% sporadic CA were diagnosed. So far, 32 patients (24 CA and 8 HSP) were further assessed by NGS gene panels, and 34.4% were diagnosed, including 29.2% CA and 50% HSP patients. Eleven novel gene variants classified as (likely) pathogenic were identified. Our results support the role of experienced clinicians in the diagnostic assessment and the clinical research of CA and HSP even in the next generation era.
Collapse
|
20
|
DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children. CHILDREN-BASEL 2021; 8:children8020092. [PMID: 33572947 PMCID: PMC7912017 DOI: 10.3390/children8020092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
DNA methylation levels are associated with neurodevelopment. Attention-deficit/hyperactivity disorder (ADHD), characterized by attention deficits, is a common neurodevelopmental disorder. We used methylation microarray and pyrosequencing to detect peripheral blood DNA methylation markers of ADHD. DNA methylation profiling data from the microarray assays identified potential differentially methylated CpG sites between 12 ADHD patients and 9 controls. Five candidate CpG sites (cg00446123, cg20513976, cg07922513, cg17096979, and cg02506324) in four genes (LIME1, KCNAB2, CAPN9, and SPTBN2) were further examined with pyrosequencing. The attention of patients were tested using the Conners’ Continuous Performance Test (CPT). In total, 126 ADHD patients with a mean age of 9.2 years (78.6% males) and 72 healthy control subjects with a mean age of 9.3 years (62.5% males) were recruited. When all participants were categorized by their CPT performance, the DNA methylation levels in LIME1 (cg00446123 and cg20513976) were found to be significantly higher and those in SPTBN2 (cg02506324) were significantly lower in children with worse CPT performance. Therefore, DNA methylation of two CpG sites in LIME1 and one CpG site in SPTBN2 is associated with attention deficits in children. DNA methylation biomarkers may assist in identifying attention deficits of children in clinical settings.
Collapse
|
21
|
Kim M, Kim AR, Kim JS, Park J, Youn J, Ahn JH, Mun JK, Lee C, Kim NS, Kim NK, Park WY, Cho JW. Clarification of undiagnosed ataxia using whole-exome sequencing with clinical implications. Parkinsonism Relat Disord 2020; 80:58-64. [DOI: 10.1016/j.parkreldis.2020.08.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/05/2020] [Accepted: 08/31/2020] [Indexed: 01/01/2023]
|
22
|
|
23
|
Pedroso JL, de Rezende Pinto WBV, Barsottini OGP, Oliveira ASB. Should we investigate mitochondrial disorders in progressive adult-onset undetermined ataxias? CEREBELLUM & ATAXIAS 2020; 7:13. [PMID: 32922825 PMCID: PMC7444269 DOI: 10.1186/s40673-020-00122-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/28/2022]
Abstract
Background Despite the broad development of next-generation sequencing approaches recently, such as whole-exome sequencing, diagnostic workup of adult-onset progressive cerebellar ataxias without remarkable family history and with negative genetic panel testing for SCAs remains a complex and expensive clinical challenge. Case presentation In this article, we report a Brazilian man with adult-onset slowly progressive pure cerebellar ataxia, which developed neuropathy and hearing loss after fifteen years of ataxia onset, in which a primary mitochondrial DNA defect (MERRF syndrome - myoclonus epilepsy with ragged-red fibers) was confirmed through muscle biopsy evaluation and whole-exome sequencing. Conclusions Mitochondrial disorders are a clinically and genetically complex and heterogenous group of metabolic diseases, resulting from pathogenic variants in the mitochondrial DNA or nuclear DNA. In our case, a correlation with histopathological changes identified on muscle biopsy helped to clarify the definitive diagnosis. Moreover, in neurodegenerative and neurogenetic disorders, some symptoms may be evinced later during disease course. We suggest that late-onset and adult pure undetermined ataxias should be considered and investigated for mitochondrial disorders, particularly MERRF syndrome and other primary mitochondrial DNA defects, together with other more commonly known nuclear genes.
Collapse
Affiliation(s)
- José Luiz Pedroso
- Ataxia Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), Pedro de Toledo Street, 650. ZIP CODE: 04039-002. Vila Clementino, São Paulo, SP Brazil
| | | | - Orlando Graziani Povoas Barsottini
- Ataxia Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), Pedro de Toledo Street, 650. ZIP CODE: 04039-002. Vila Clementino, São Paulo, SP Brazil
| | - Acary Souza Bulle Oliveira
- Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP Brazil
| |
Collapse
|
24
|
Inherited Cerebellar Ataxias: 5-Year Experience of the Irish National Ataxia Clinic. THE CEREBELLUM 2020; 20:54-61. [PMID: 32816195 DOI: 10.1007/s12311-020-01180-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Establishing a molecular diagnosis in patients with progressive ataxia is often challenging due to significant genetic and clinical heterogeneity and requires a methodical approach with expert clinical evaluation and investigations. We describe the 5-year experience of the National Ataxia Clinic (NAC), Ireland. All adults with ataxia attending the NAC between 2014 and 2019 were evaluated. All individuals underwent detailed clinical assessment and investigations including, where appropriate, genetic testing using next-generation sequencing. For all patients, acquired causes were ruled out. A total of 254 patients from 196 families were assessed; with growth of the clinic cohort by 82% from 133 to 242 over the 5-year period. The underlying genetic cause was identified in 128/196 probands (65.3%). The detection rate for repeat expansion disorder gene testing was 47.7% (82/172) and using NGS gene panel, a genetic diagnosis was obtained in 30/84 (35.7%). Whole exome sequencing identified the molecular diagnosis in 4/20 (20%), and whole genome sequencing provided genetic diagnosis in 1/5 (20%). The commonest diagnosis was Friedreich's ataxia (68/128, 53.1%). SPG7-associated ataxia was the second most common diagnosis (21/128, 16.4%), followed by ANO10-associated spastic ataxia, ataxia telangiectasia (AT), and other rarer phenotypes. Our results highlight that careful clinical phenotyping in a dedicated ataxia clinic is crucial for appropriate genetic testing in selected patients in a timely manner. Advanced genetic testing has significantly improved the diagnostic yield in patients with suspected genetic ataxia and should be considered in all individuals with negative repeat expansion testing.
Collapse
|
25
|
Novis LE, Spitz M, Jardim M, Raskin S, Teive HAG. Evidence and practices of the use of next generation sequencing in patients with undiagnosed autosomal dominant cerebellar ataxias: a review. ARQUIVOS DE NEURO-PSIQUIATRIA 2020; 78:576-585. [PMID: 32725052 DOI: 10.1590/0004-282x20200017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/28/2020] [Indexed: 11/22/2022]
Abstract
Autosomal dominant cerebellar ataxias (ADCA) are heterogeneous diseases with a highly variable phenotype and genotype. They can be divided into episodic ataxia and spinocerebellar ataxia (SCA); the latter is considered the prototype of the ADCA. Most of the ADCA are caused by polyglutamine expansions, mainly SCA 1, 2, 3, 6, 7, 17 and Dentatorubral-pallidoluysian atrophy (DRPLA). However, 30% of patients remain undiagnosed after testing for these most common SCA. Recently, several studies have demonstrated that the new generation of sequencing methods are useful for the diagnose of these patients. This review focus on searching evidence on the literature, its usefulness in clinical practice and future perspectives.
Collapse
Affiliation(s)
- Luiz Eduardo Novis
- Universidade do Estado do Rio de Janeiro, Hospital Universitário Pedro Ernesto, Serviço de Neurologia, Rio de Janeiro RJ, Brazil
| | - Mariana Spitz
- Universidade do Estado do Rio de Janeiro, Hospital Universitário Pedro Ernesto, Serviço de Neurologia, Rio de Janeiro RJ, Brazil
| | - Marcia Jardim
- Universidade do Estado do Rio de Janeiro, Hospital Universitário Pedro Ernesto, Serviço de Neurologia, Rio de Janeiro RJ, Brazil
| | | | - Hélio A G Teive
- Universidade Federal do Paraná, Departamento de Clínica Médica, Serviço de Neurologia, Setor de Distúrbios do Movimento, Hospital das Clínicas, Curitiba PR, Brazil
| |
Collapse
|
26
|
Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
Collapse
Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| |
Collapse
|
27
|
Perez Maturo J, Zavala L, Vega P, González-Morón D, Medina N, Salinas V, Rosales J, Córdoba M, Arakaki T, Garretto N, Rodríguez-Quiroga S, Kauffman MA. Overwhelming genetic heterogeneity and exhausting molecular diagnostic process in chronic and progressive ataxias: facing it up with an algorithm, a gene, a panel at a time. J Hum Genet 2020; 65:895-902. [DOI: 10.1038/s10038-020-0785-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
|
28
|
Street D, O'Driscoll M, Taylor M, Nicholl D. Late-onset ataxia plus syndromes. Neurol Clin Pract 2020; 10:e22-e24. [DOI: 10.1212/cpj.0000000000000707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/07/2019] [Indexed: 11/15/2022]
|
29
|
Comprehensive Exonic Sequencing of Known Ataxia Genes in Episodic Ataxia. Biomedicines 2020; 8:biomedicines8050134. [PMID: 32466254 PMCID: PMC7277596 DOI: 10.3390/biomedicines8050134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 01/09/2023] Open
Abstract
Episodic Ataxias (EAs) are a small group (EA1–EA8) of complex neurological conditions that manifest as incidents of poor balance and coordination. Diagnostic testing cannot always find causative variants for the phenotype, however, and this along with the recently proposed EA type 9 (EA9), suggest that more EA genes are yet to be discovered. We previously identified disease-causing mutations in the CACNA1A gene in 48% (n = 15) of 31 patients with a suspected clinical diagnosis of EA2, and referred to our laboratory for CACNA1A gene testing, leaving 52% of these cases (n = 16) with no molecular diagnosis. In this study, whole exome sequencing (WES) was performed on 16 patients who tested negative for CACNA1A mutations. Tiered analysis of WES data was performed to first explore (Tier-1) the ataxia and ataxia-associated genes (n = 170) available in the literature and databases for comprehensive EA molecular genetic testing; we then investigated 353 ion channel genes (Tier-2). Known and potential causal variants were identified in n = 8/16 (50%) patients in 8 genes (SCN2A, p.Val1325Phe; ATP1A3, p.Arg756His; PEX7, p.Tyr40Ter; and KCNA1, p.Arg167Met; CLCN1, p.Gly945ArgfsX39; CACNA1E, p.Ile614Val; SCN1B, p.Cys121Trp; and SCN9A, p.Tyr1217Ter). These results suggest that mutations in these genes might cause an ataxia phenotype or that combinations of more than one mutation contribute to ataxia disorders.
Collapse
|
30
|
Doble B, Schofield D, Evans CA, Groza T, Mattick JS, Field M, Roscioli T. Impacts of genomics on the health and social costs of intellectual disability. J Med Genet 2020; 57:479-486. [PMID: 31980565 DOI: 10.1136/jmedgenet-2019-106445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND This study provides an integrated assessment of the economic and social impacts of genomic sequencing for the detection of monogenic disorders resulting in intellectual disability (ID). METHODS Multiple knowledge bases were cross-referenced and analysed to compile a reference list of monogenic disorders associated with ID. Multiple literature searches were used to quantify the health and social costs for the care of people with ID. Health and social expenditures and the current cost of whole-exome sequencing and whole-genome sequencing were quantified in relation to the more common causes of ID and their impact on lifespan. RESULTS On average, individuals with ID incur annual costs in terms of health costs, disability support, lost income and other social costs of US$172 000, accumulating to many millions of dollars over a lifetime. CONCLUSION The diagnosis of monogenic disorders through genomic testing provides the opportunity to improve the diagnosis and management, and to reduce the costs of ID through informed reproductive decisions, reductions in unproductive diagnostic tests and increasingly targeted therapies.
Collapse
Affiliation(s)
- Brett Doble
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia .,Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Deborah Schofield
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,GenImpact, School of Economics, Faculty of Business and Economics, Macquarie University, Sydney, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Tudor Groza
- Pryzm Health, Gold Coast, Queensland, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Mike Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia.,NSW Health Pathology East Laboratory, Prince of Wales Private Hospital, Randwick, New South Wales, Australia
| |
Collapse
|
31
|
Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
Collapse
|
32
|
Genetic and phenotypic features of patients with childhood ataxias diagnosed by next-generation sequencing gene panel. Brain Dev 2020; 42:6-18. [PMID: 31493945 DOI: 10.1016/j.braindev.2019.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The purpose of this prospective study was to identify the characteristics of pediatric recessive ataxias and the mutations leading to them. METHODS Eighty-four pediatric patients aged 0-18 years presenting to our clinic, evaluated by means of imaging, metabolic or pathological investigation, or single-gene test, in whom Friedreich's ataxia was excluded, and predicted to carry the progressive autosomal recessive ataxia gene were included in the study. Patients' demographic, clinical, laboratory, and radiological characteristics were recorded. DNA and panel sequencing directed toward ataxia-related genes was performed using the next-generation sequencing method. RESULTS A molecular diagnosis was established in 21 (25%) of the 84 patients. Genetically, infantile neuroaxonal dystrophy (7/21), ataxia with oculomotor apraxia type 1 (5/21), neuronal ceroid lipofuscinosis type 5 (2/21), ataxia with oculomotor apraxia type 2 (1/21), Lafora disease (1/21), tremor ataxia syndrome accompanying central hypomyelination (1/21), Charlevoix-Saguenay ataxia (1/21), Marinesco-Sjögren syndrome (1/21), VLDRL-associated cerebellar hypoplasia (1/21), and TSEN54-related pontocerebellar hypoplasia (1/21) mutations were detected. CONCLUSIONS Approximately 25% of our patients were diagnosed. Novel mutations in the known genes were identified and are important in terms of phenotype-genotype correlation.
Collapse
|
33
|
Beaudin M, Matilla-Dueñas A, Soong BW, Pedroso JL, Barsottini OG, Mitoma H, Tsuji S, Schmahmann JD, Manto M, Rouleau GA, Klein C, Dupre N. The Classification of Autosomal Recessive Cerebellar Ataxias: a Consensus Statement from the Society for Research on the Cerebellum and Ataxias Task Force. CEREBELLUM (LONDON, ENGLAND) 2019; 18:1098-1125. [PMID: 31267374 PMCID: PMC6867988 DOI: 10.1007/s12311-019-01052-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is currently no accepted classification of autosomal recessive cerebellar ataxias, a group of disorders characterized by important genetic heterogeneity and complex phenotypes. The objective of this task force was to build a consensus on the classification of autosomal recessive ataxias in order to develop a general approach to a patient presenting with ataxia, organize disorders according to clinical presentation, and define this field of research by identifying common pathogenic molecular mechanisms in these disorders. The work of this task force was based on a previously published systematic scoping review of the literature that identified autosomal recessive disorders characterized primarily by cerebellar motor dysfunction and cerebellar degeneration. The task force regrouped 12 international ataxia experts who decided on general orientation and specific issues. We identified 59 disorders that are classified as primary autosomal recessive cerebellar ataxias. For each of these disorders, we present geographical and ethnical specificities along with distinctive clinical and imagery features. These primary recessive ataxias were organized in a clinical and a pathophysiological classification, and we present a general clinical approach to the patient presenting with ataxia. We also identified a list of 48 complex multisystem disorders that are associated with ataxia and should be included in the differential diagnosis of autosomal recessive ataxias. This classification is the result of a consensus among a panel of international experts, and it promotes a unified understanding of autosomal recessive cerebellar disorders for clinicians and researchers.
Collapse
Affiliation(s)
- Marie Beaudin
- Axe Neurosciences, CHU de Québec-Université Laval, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Antoni Matilla-Dueñas
- Department of Neuroscience, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Bing-Weng Soong
- Department of Neurology, Shuang Ho Hospital and Taipei Neuroscience Institute, Taipei Medical University, Taipei, Taiwan, Republic of China
- National Yang-Ming University School of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
| | - Jose Luiz Pedroso
- Ataxia Unit, Department of Neurology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Orlando G Barsottini
- Ataxia Unit, Department of Neurology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Hiroshi Mitoma
- Medical Education Promotion Center, Tokyo Medical University, Tokyo, Japan
| | - Shoji Tsuji
- The University of Tokyo, Tokyo, Japan
- International University of Health and Welfare, Chiba, Japan
| | - Jeremy D Schmahmann
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mario Manto
- Service de Neurologie, Médiathèque Jean Jacquy, CHU-Charleroi, 6000, Charleroi, Belgium
- Service des Neurosciences, UMons, Mons, Belgium
| | | | | | - Nicolas Dupre
- Axe Neurosciences, CHU de Québec-Université Laval, Québec, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
| |
Collapse
|
34
|
Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
Collapse
Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| |
Collapse
|
35
|
Mutlu-Albayrak H, Kırat E, Gürbüz G. Childhood-onset autosomal recessive ataxias: a cross-sectional study from Turkey. Neurogenetics 2019; 21:59-66. [PMID: 31741144 DOI: 10.1007/s10048-019-00597-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 10/30/2019] [Indexed: 01/12/2023]
Abstract
Autosomal recessive ataxias (ARAs) are a heterogeneous group of inherited neurodegenerative disorders that affect the cerebellum, the spinocerebellar tract, and/or the sensory tracts of the spinal cord. This study is aimed at establishing molecular classification and phenotypic correlation of childhood-onset ARAs in Southeast Anatolia of Turkey. Sixty-five children (aged 0 to 18) from 40 unrelated families who were analyzed through hereditary ataxia NGS panel between the years of 2015-2018 were selected for the study. Seventeen different, clinically significant ARA-related pathogenic variants were detected in 33 of 40 families (82.5%), 12 of which were noted to be unreported variants. Among these 33 families, 24 had ATM-related (72.72%), four had SACS-related (12.12%), three had COQ8A-related (9.09%), and two had APTX-related (6.06%) pathogenic variants. The c.3576G>A (p.K1192=) was the most common homozygous pathogenic ATM variant (33.33%) that was associated with milder phenotype of ataxia telangiectasia (AT) with the onset of age of 3. Patients with SACS variants demonstrated developmental delay and progressive ataxia before the age of 3. Slowly progressive ataxia and intellectual disability were the common clinical manifestations of the patients with homozygous c.1396delG (p. E466Rfs*11) pathogenic variant in COQ8A. Homozygous APTX c.689T>G (p.V230G) pathogenic variant was identified in two patients who had chief complaint of ataxic gait onset after puberty. The most common types of ARAs in this region are AT- and Charlevoix-Saguenay-type spastic ataxia. ATM gene analysis should be performed foremost on children presenting early-onset ataxia from Southeastern Anatolia. If there is a concomitant peripheral neuron involvement, SACS gene analysis should be preferred. This valuable data will be a guide for the first step molecular diagnostic approach before requesting the NGS panel for ARA.
Collapse
Affiliation(s)
- Hatice Mutlu-Albayrak
- Department of Pediatric Genetics, Cengiz Gökcek Maternity & Children's Hospital, 15 Temmuz mh. 62 nolu cd, 27010, Gaziantep, Turkey.
| | - Emre Kırat
- Department of Medical Genetics, Ersin Arslan Education and Research Hospital, Gaziantep, Turkey
| | - Gürkan Gürbüz
- Department of Pediatric Neurology, Cengiz Gökcek Maternity & Children's Hospital, Gaziantep, Turkey
| |
Collapse
|
36
|
Nuzhnyi EP, Abramycheva NY, Klyushnikov SA, Seliverstov YA, Vetchinova AS, Pogoda TV, Ershova MV, Fedotova EY, Illarioshkin SN. [Diagnostic algorithm for autosomal recessive ataxia]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:74-82. [PMID: 31626222 DOI: 10.17116/jnevro201911909174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AIM To develop a complex algorithm for autosomal recessive ataxia (ARA) diagnosis applicable for Russian patients with degenerative ataxias. MATERIAL AND METHODS 48 patients with of presumably degenerative ataxias were examined. Clinical evaluation was performed with the use of the SARA and ICARS scales (for ataxia) and MoCA (cognitive functions), and a set of laboratory tests was carried out, including electromyography, brain MRI, and DNA analysis of mutations responsible for Friedreich's disease and spinocerebellar ataxias (SCAs) types 1, 2, 3, 6 and 17. 28 patients underwent mutation screening using a multigenic MPS panel. RESULTS 8 patients (16.7%) with non-hereditary causes of ataxia were identified: cerebellar alcoholic degeneration (n = 6) and multiple system atrophy of cerebellar type (n = 2); 3 patients (6.3%) with genetic ataxias were identified using routine DNA tests, such as with SCA type 1, 2 and 17, and 9 (18.8%) patients with Friedreich's disease. The MPS panel enabled molecular diagnosis of ARA in 8 patients (28.6%): ataxia-telangiectasia (n = 2), SANDO syndrome (n = 2), ataxia with oculomotor apraxia type 2 (n = 1), SCAR10 (n = 1), SCAR16 (n = 1), and atypical form of neuroaxonal dystrophy (n = 1). The diagnosis was not established in 20 patients. CONCLUSION We have proposed an appropriate algorithm for degenerative ataxia diagnosis which is recommended to be used when examining patients with sporadic and autosomal recessive cases of the disorders with dyscoordination of movements.
Collapse
Affiliation(s)
- E P Nuzhnyi
- Research Center of Neurology, Moscow, Russia
| | | | | | | | | | - T V Pogoda
- Research Center of Neurology, Moscow, Russia
| | - M V Ershova
- Research Center of Neurology, Moscow, Russia
| | | | | |
Collapse
|
37
|
Coutelier M, Hammer MB, Stevanin G, Monin ML, Davoine CS, Mochel F, Labauge P, Ewenczyk C, Ding J, Gibbs JR, Hannequin D, Melki J, Toutain A, Laugel V, Forlani S, Charles P, Broussolle E, Thobois S, Afenjar A, Anheim M, Calvas P, Castelnovo G, de Broucker T, Vidailhet M, Moulignier A, Ghnassia RT, Tallaksen C, Mignot C, Goizet C, Le Ber I, Ollagnon-Roman E, Pouget J, Brice A, Singleton A, Durr A. Efficacy of Exome-Targeted Capture Sequencing to Detect Mutations in Known Cerebellar Ataxia Genes. JAMA Neurol 2019; 75:591-599. [PMID: 29482223 DOI: 10.1001/jamaneurol.2017.5121] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Importance Molecular diagnosis is difficult to achieve in disease groups with a highly heterogeneous genetic background, such as cerebellar ataxia (CA). In many patients, candidate gene sequencing or focused resequencing arrays do not allow investigators to reach a genetic conclusion. Objectives To assess the efficacy of exome-targeted capture sequencing to detect mutations in genes broadly linked to CA in a large cohort of undiagnosed patients and to investigate their prevalence. Design, Setting, and Participants Three hundred nineteen index patients with CA and without a history of dominant transmission were included in the this cohort study by the Spastic Paraplegia and Ataxia Network. Centralized storage was in the DNA and cell bank of the Brain and Spine Institute, Salpetriere Hospital, Paris, France. Patients were classified into 6 clinical groups, with the largest being those with spastic ataxia (ie, CA with pyramidal signs [n = 100]). Sequencing was performed from January 1, 2014, through December 31, 2016. Detected variants were classified as very probably or definitely causative, possibly causative, or of unknown significance based on genetic evidence and genotype-phenotype considerations. Main Outcomes and Measures Identification of variants in genes broadly linked to CA, classified in pathogenicity groups. Results The 319 included patients had equal sex distribution (160 female [50.2%] and 159 male patients [49.8%]; mean [SD] age at onset, 27.9 [18.6] years). The age at onset was younger than 25 years for 131 of 298 patients (44.0%) with complete clinical information. Consanguinity was present in 101 of 298 (33.9%). Very probable or definite diagnoses were achieved for 72 patients (22.6%), with an additional 19 (6.0%) harboring possibly pathogenic variants. The most frequently mutated genes were SPG7 (n = 14), SACS (n = 8), SETX (n = 7), SYNE1 (n = 6), and CACNA1A (n = 6). The highest diagnostic rate was obtained for patients with an autosomal recessive CA with oculomotor apraxia-like phenotype (6 of 17 [35.3%]) or spastic ataxia (35 of 100 [35.0%]) and patients with onset before 25 years of age (41 of 131 [31.3%]). Peculiar phenotypes were reported for patients carrying KCND3 or ERCC5 variants. Conclusions and Relevance Exome capture followed by targeted analysis allows the molecular diagnosis in patients with highly heterogeneous mendelian disorders, such as CA, without prior assumption of the inheritance mode or causative gene. Being commonly available without specific design need, this procedure allows testing of a broader range of genes, consequently describing less classic phenotype-genotype correlations, and post hoc reanalysis of data as new genes are implicated in the disease.
Collapse
Affiliation(s)
- Marie Coutelier
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Laboratory of Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres Research University, Paris, France
| | - Monia B Hammer
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Giovanni Stevanin
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres Research University, Paris, France.,Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marie-Lorraine Monin
- Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire-Sophie Davoine
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres Research University, Paris, France
| | - Fanny Mochel
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Pierre Labauge
- Service de Neurologie, Hopital Gui de Chauliac, Centre Hospitalier Universitaire (CHU) de Montpellier, Montpellier, France
| | - Claire Ewenczyk
- Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Didier Hannequin
- Service de Génétique, Service de Neurologie, INSERM U1079, Rouen University Hospital, Rouen, France
| | - Judith Melki
- UMR 1169, INSERM and University Paris Saclay, Le Kremlin Bicêtre, France.,Medical Genetics Unit, Centre Hospitalier Sud-Francilien, Corbeil Essonnes, France
| | - Annick Toutain
- Service de Génétique, Centre Hospitalier Universitaire de Tours, INSERM U930, Faculté de Médecine, Université François Rabelais, Tours, France
| | - Vincent Laugel
- Service de Pédiatrie 1, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Sylvie Forlani
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France
| | - Perrine Charles
- Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Emmanuel Broussolle
- Service de Neurologie C, Hôpital Neurologique Pierre-Wertheimer, Hospices Civils de Lyon, Bron, France.,Centre de Neurosciences Cognitives, Centre National de la Recherche Scientifique (CNRS)-UMR 5229, Bron, France.,Université de Lyon, Université Claude-Bernard-Lyon I, Villeurbanne, France
| | - Stéphane Thobois
- Service de Neurologie C, Hôpital Neurologique Pierre-Wertheimer, Hospices Civils de Lyon, Bron, France.,Centre de Neurosciences Cognitives, Centre National de la Recherche Scientifique (CNRS)-UMR 5229, Bron, France.,Université de Lyon, Université Claude-Bernard-Lyon I, Villeurbanne, France
| | - Alexandra Afenjar
- Service de Génétique et Centre de Référence Pour les Malformations et les Maladies Congénitales du Cervelet, AP-HP, Paris, France
| | - Mathieu Anheim
- Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Strasbourg, France.,Département de Neurologie, Hôpital de Hautepierre, CHU de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS-UMR 7104, Université de Strasbourg, Illkirch, France
| | - Patrick Calvas
- Service de Génétique Médicale, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | | | - Thomas de Broucker
- Service de Neurologie, Centre Hospitalier de Saint-Denis, Saint-Denis, France
| | - Marie Vidailhet
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Département des Maladies du Système Nerveux, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | - Antoine Moulignier
- Service de Neurologie, Fondation Ophtalmologique A. de Rothschild, Paris, France
| | | | - Chantal Tallaksen
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,currently affiliated with Department of Neurology, Oslo University Hospital; and Faculty of Medicine, Oslo University, Oslo, Norway
| | - Cyril Mignot
- Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | - Cyril Goizet
- Laboratoire Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France.,Service de Génétique Médicale, CHU Pellegrin, Bordeaux, France
| | - Isabelle Le Ber
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France
| | | | - Jean Pouget
- Centre de Référence des Maladies Neuromusculaires et de la Sclérose Latérale Amyotrophique, Assistance Publique-Hôpitaux de Marseille, Aix Marseille Université, Hôpital de La Timone, Marseille, France
| | - Alexis Brice
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Alexandra Durr
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1127, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche (UMR) 7225, Paris, France.,Unité Mixte de Recherche en Santé 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Paris, France.,Institut du Cerveau et de la Moelle Epinière, Paris, France.,Centre de Référence de Neurogénétique, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | |
Collapse
|
38
|
Sutherland HG, Albury CL, Griffiths LR. Advances in genetics of migraine. J Headache Pain 2019; 20:72. [PMID: 31226929 PMCID: PMC6734342 DOI: 10.1186/s10194-019-1017-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Background Migraine is a complex neurovascular disorder with a strong genetic component. There are rare monogenic forms of migraine, as well as more common polygenic forms; research into the genes involved in both types has provided insights into the many contributing genetic factors. This review summarises advances that have been made in the knowledge and understanding of the genes and genetic variations implicated in migraine etiology. Findings Migraine is characterised into two main types, migraine without aura (MO) and migraine with aura (MA). Hemiplegic migraine is a rare monogenic MA subtype caused by mutations in three main genes - CACNA1A, ATP1A2 and SCN1A - which encode ion channel and transport proteins. Functional studies in cellular and animal models show that, in general, mutations result in impaired glutamatergic neurotransmission and cortical hyperexcitability, which make the brain more susceptible to cortical spreading depression, a phenomenon thought to coincide with aura symptoms. Variants in other genes encoding ion channels and solute carriers, or with roles in regulating neurotransmitters at neuronal synapses, or in vascular function, can also cause monogenic migraine, hemiplegic migraine and related disorders with overlapping symptoms. Next-generation sequencing will accelerate the finding of new potentially causal variants and genes, with high-throughput bioinformatics analysis methods and functional analysis pipelines important in prioritising, confirming and understanding the mechanisms of disease-causing variants. With respect to common migraine forms, large genome-wide association studies (GWAS) have greatly expanded our knowledge of the genes involved, emphasizing the role of both neuronal and vascular pathways. Dissecting the genetic architecture of migraine leads to greater understanding of what underpins relationships between subtypes and comorbid disorders, and may have utility in diagnosis or tailoring treatments. Further work is required to identify causal polymorphisms and the mechanism of their effect, and studies of gene expression and epigenetic factors will help bridge the genetics with migraine pathophysiology. Conclusions The complexity of migraine disorders is mirrored by their genetic complexity. A comprehensive knowledge of the genetic factors underpinning migraine will lead to improved understanding of molecular mechanisms and pathogenesis, to enable better diagnosis and treatments for migraine sufferers.
Collapse
Affiliation(s)
- Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation. School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, Institute of Health and Biomedical Innovation. School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation. School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia.
| |
Collapse
|
39
|
Kang C, Liang C, Ahmad KE, Gu Y, Siow SF, Colebatch JG, Whyte S, Ng K, Cremer PD, Corbett AJ, Davis RL, Roscioli T, Cowley MJ, Park JS, Sue CM, Kumar KR. High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia. THE CEREBELLUM 2019; 18:137-146. [PMID: 30078120 DOI: 10.1007/s12311-018-0969-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic testing strategies such as next-generation sequencing (NGS) panels and whole genome sequencing (WGS) can be applied to the hereditary cerebellar ataxias (HCAs), but their exact role in the diagnostic pathway is unclear. We aim to determine the yield from genetic testing strategies and the genetic and phenotypic spectrum of HCA in Australia by analysing real-world data. We performed a retrospective review on 87 HCA cases referred to the Neurogenetics Clinic at the Royal North Shore Hospital, Sydney, Australia. Probands underwent triplet repeat expansion testing; those that tested negative had NGS-targeted panels and WGS testing when available. In our sample, 58.6% were male (51/87), with an average age at onset of 37.1 years. Individuals with sequencing variants had a prolonged duration of illness compared to those with a triplet repeat expansion. The detection rate in probands for routine repeat expansion panels was 13.8% (11/80). NGS-targeted panels yielded a further 11 individuals (11/32, 34.4%), with WGS yielding 1 more diagnosis (1/3, 33.3%). NGS panels and WGS improved the overall diagnostic rate to 28.8% (23/80) in 14 known HCA loci. The genetic findings included novel variants in ANO10, CACNA1A, PRKCG and SPG7. Our findings highlight the genetic heterogeneity of HCAs and support the use of NGS approaches for individuals who were negative on repeat expansion testing. In comparison to repeat disorders, individuals with sequencing variants may have a prolonged duration of illness, consistent with slower progression of disease.
Collapse
Affiliation(s)
- Ce Kang
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia
| | - Christina Liang
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kate E Ahmad
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Yufan Gu
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Sue-Faye Siow
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - James G Colebatch
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, Australia
| | - Scott Whyte
- Department of Neurology, Gosford Hospital, Gosford, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Philip D Cremer
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Alastair J Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, Australia
| | - Ryan L Davis
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia.,Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia
| | - Tony Roscioli
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Department of Clinical Genetics, Sydney Children's Hospital, Randwick, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Jin-Sung Park
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Experimental Animal Research, Seoul National University Hospital, Biomedical Research Institute, Seoul, Republic of Korea
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia. .,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia. .,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
| |
Collapse
|
40
|
de Silva RN, Vallortigara J, Greenfield J, Hunt B, Giunti P, Hadjivassiliou M. Diagnosis and management of progressive ataxia in adults. Pract Neurol 2019; 19:196-207. [PMID: 31048364 PMCID: PMC6585307 DOI: 10.1136/practneurol-2018-002096] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Progressive ataxia in adults can be difficult to diagnose, owing to its heterogeneity and the rarity of individual causes. Many patients remain undiagnosed (‘idiopathic’ ataxia). This paper provides suggested diagnostic pathways for the general neurologist, based on Ataxia UK’s guidelines for professionals. MR brain scanning can provide diagnostic clues, as well as identify ‘structural’ causes such as tumours and multiple sclerosis. Advances in molecular genetics, including the wider and cheaper availability of ‘next-generation sequencing’, have enabled clinicians to identify many more cases with a genetic cause. Finally, autoimmunity is probably an under-recognised cause of progressive ataxia: as well as patients with antigliadin antibodies there are smaller numbers with various antibodies, including some associated with cancer. There are a few treatable ataxias, but also symptomatic treatments to help people with the spectrum of complications that might accompany progressive ataxias. Multidisciplinary team involvement and allied health professionals’ input are critical to excellent patient care, including in the palliative phase. We can no longer justify a nihilistic approach to the management of ataxia.
Collapse
Affiliation(s)
| | | | | | | | - Paola Giunti
- Department of Clinical and Movement Neurosciences, Ataxia Centre, UCL Institute of Neurology, London, UK
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, UK
| |
Collapse
|
41
|
Integrated Analysis of Whole Exome Sequencing and Copy Number Evaluation in Parkinson's Disease. Sci Rep 2019; 9:3344. [PMID: 30833663 PMCID: PMC6399448 DOI: 10.1038/s41598-019-40102-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
Genetic studies of the familial forms of Parkinson’s disease (PD) have identified a number of causative genes with an established role in its pathogenesis. These genes only explain a fraction of the diagnosed cases. The emergence of Next Generation Sequencing (NGS) expanded the scope of rare variants identification in novel PD related genes. In this study we describe whole exome sequencing (WES) genetic findings of 60 PD patients with 125 variants validated in 51 of these cases. We used strict criteria for variant categorization that generated a list of variants in 20 genes. These variants included loss of function and missense changes in 18 genes that were never previously linked to PD (NOTCH4, BCOR, ITM2B, HRH4, CELSR1, SNAP91, FAM174A, BSN, SPG7, MAGI2, HEPHL1, EPRS, PUM1, CLSTN1, PLCB3, CLSTN3, DNAJB9 and NEFH) and 2 genes that were previously associated with PD (EIF4G1 and ATP13A2). These genes either play a critical role in neuronal function and/or have mouse models with disease related phenotypes. We highlight NOTCH4 as an interesting candidate in which we identified a deleterious truncating and a splice variant in 2 patients. Our combined molecular approach provides a comprehensive strategy applicable for complex genetic disorders.
Collapse
|
42
|
Application of next generation sequencing technology on contamination monitoring in microbiology laboratory. BIOSAFETY AND HEALTH 2019; 1:25-31. [PMID: 32501441 PMCID: PMC7148601 DOI: 10.1016/j.bsheal.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.
Collapse
|
43
|
Daoud H, Ghani M, Nfonsam L, Potter R, Ordorica S, Haslett V, Santos N, Derksen H, Lahey D, McGill M, Trudel V, Antoniuk B, Vasli N, Chisholm C, Mettler G, Sinclair-Bourque E, McGowan-Jordan J, Smith A, Roberts R, Jarinova O. Genetic Diagnostic Testing for Inherited Cardiomyopathies: Considerations for Offering Multi-Gene Tests in a Health Care Setting. J Mol Diagn 2019; 21:437-448. [PMID: 30731207 DOI: 10.1016/j.jmoldx.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/16/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes and expanded our panel by fivefold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identified by NGS, which reduces the cost and time of testing. The NGS assay was developed for the simultaneous analysis of 45 IC genes and was assessed for the impact of panel expansion on variant detection, turnaround time, and cost of testing in a cohort of 993 patients. The assay led to a considerable reduction in test cost and turnaround time. However, only a marginal increase was observed in the diagnostic yield, whereas the rate of inconclusive findings increased considerably. These findings suggest that the ongoing evaluation of gene content and monitoring of clinical utility for multi-gene tests are essential to achieve maximum clinical utility of multi-gene tests in a publicly funded health care setting.
Collapse
Affiliation(s)
- Hussein Daoud
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.
| | - Mahdi Ghani
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Landry Nfonsam
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ryan Potter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Shelley Ordorica
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Virginia Haslett
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nathaniel Santos
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Heather Derksen
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Donelda Lahey
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Martha McGill
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Vanessa Trudel
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Brittany Antoniuk
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nasim Vasli
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gabrielle Mettler
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Jean McGowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda Smith
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Roberts
- University of Arizona College of Medicine, Tucson, Arizona
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
| |
Collapse
|
44
|
Farias AM, Appenzeller S, França MC, Martinez AR, Etchebehere EE, Souza TF, Santos AO. Assessment of Bone Mineral Density of Patients with Spinocerebellar Ataxia Type 3. J Mov Disord 2019; 12:43-46. [PMID: 30732432 PMCID: PMC6369376 DOI: 10.14802/jmd.18041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/13/2018] [Indexed: 12/19/2022] Open
Abstract
Objective Machado-Joseph disease (MJD) is a spinocerebellar ataxia, and osteoporosis is a multifactor disease that may affect patients with neurologic conditions. The frequency of osteoporosis among MJD patients, however, has not been studied. The purpose of this study is to evaluate bone mineral density (BMD) and identify correlations between clinical factors and frequency of vertebral fractures in patients with MJD. Methods Clinical data, lumbar X-rays and BMD data were obtained in 30 patients with MJD. Results Ten patients (33.3%) showed low BMD in at least one of the sites studied based on Z-scores. The Z-score correlated directly with body mass index, and the femoral neck Z-score was inversely correlated with cytosine-adenine-guanine (CAG) expansion. There was no correlation between BMD and other clinical factors. Forty-three percent of the patients reported previous pathologic fractures. Five patients (16.7%) had at least one fracture detected by lumbar X-ray. Conclusion Low BMD and fractures are frequent among MJD patients, and careful management of BMD may be beneficial for these patients.
Collapse
Affiliation(s)
- Aline Ms Farias
- Nuclear Medicine Division, Department of Radiology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Simone Appenzeller
- Rheumatology Division, Department of Internal Medicine, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcondes C França
- Department of Neurology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Alberto Rm Martinez
- Department of Neurology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Elba E Etchebehere
- Nuclear Medicine Division, Department of Radiology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Thiago F Souza
- Department of Radiology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Allan O Santos
- Nuclear Medicine Division, Department of Radiology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| |
Collapse
|
45
|
Krygier M, Kwarciany M, Wasilewska K, Pienkowski VM, Krawczyńska N, Zielonka D, Kosińska J, Stawinski P, Rudzińska-Bar M, Boczarska-Jedynak M, Karaszewski B, Limon J, Sławek J, Płoski R, Rydzanicz M. A study in a Polish ataxia cohort indicates genetic heterogeneity and points to MTCL1 as a novel candidate gene. Clin Genet 2019; 95:415-419. [PMID: 30548255 DOI: 10.1111/cge.13489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/02/2018] [Indexed: 11/30/2022]
Abstract
Inherited ataxias are a group of highly heterogeneous, complex neurological disorders representing a significant diagnostic challenge in clinical practice. We performed a next-generation sequencing (NGS) analysis in 10 index cases with unexplained progressive cerebellar ataxia of suspected autosomal recessive inheritance. A definite molecular diagnosis was obtained in 5/10 families and included the following diseases: autosomal recessive spastic ataxia of Charlevoix-Saguenay, POLR3B-related hypomyelinating leukodystrophy, primary coenzyme Q10 deficiency type 4, Niemann-Pick disease type C1 and SYNE1-related ataxia. In addition, we found a novel homozygous MTCL1 loss of function variant p.(Lys407fs) in a 23-year-old patient with slowly progressive cerebellar ataxia, mild intellectual disability, seizures in childhood and episodic pain in the lower limbs. The identified variant is predicted to truncate the protein after first 444 of 1586 amino acids. MTCL1 encodes a microtubule-associated protein highly expressed in cerebellar Purkinje cells; its knockout in a mouse model causes ataxia. We propose MTCL1 as a candidate gene for autosomal recessive cerebellar ataxia in humans. In addition, our study confirms the high diagnostic yield of NGS in early-onset cerebellar ataxias, with at least 50% detection rate in our ataxia cohort.
Collapse
Affiliation(s)
- Magdalena Krygier
- Department of Developmental Neurology, University Clinical Centre, Medical University of Gdansk, Gdansk, Poland.,Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdansk, Gdansk, Poland
| | - Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Natalia Krawczyńska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Daniel Zielonka
- Department of Public Health, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Monika Rudzińska-Bar
- Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski Krakow University, Krakow, Poland
| | | | | | - Janusz Limon
- Polish Academy of Sciences, Gdansk, Poland.,Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Jarosław Sławek
- Neurology Department, St. Adalbert Hospital, Copernicus PL, Medical University of Gdansk, Gdansk, Poland.,Neurological and Psychiatric Nursing Department, Medical University of Gdansk, Gdansk, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | |
Collapse
|
46
|
Tankard RM, Bennett MF, Degorski P, Delatycki MB, Lockhart PJ, Bahlo M. Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data. Am J Hum Genet 2018; 103:858-873. [PMID: 30503517 PMCID: PMC6288141 DOI: 10.1016/j.ajhg.2018.10.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/16/2018] [Indexed: 10/27/2022] Open
Abstract
Repeat expansions cause more than 30 inherited disorders, predominantly neurogenetic. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single-gene or small-panel PCR-based methods can help to identify the precise genetic cause, but they can be slow and costly and often yield no result. Researchers are increasingly performing genomic analysis via whole-exome and whole-genome sequencing (WES and WGS) to diagnose genetic disorders. However, until recently, analysis protocols could not identify repeat expansions in these datasets. We developed exSTRa (expanded short tandem repeat algorithm), a method that uses either WES or WGS to identify repeat expansions. Performance of exSTRa was assessed in a simulation study. In addition, four retrospective cohorts of individuals with eleven different known repeat-expansion disorders were analyzed with exSTRa. We assessed results by comparing the findings to known disease status. Performance was also compared to three other analysis methods (ExpansionHunter, STRetch, and TREDPARSE), which were developed specifically for WGS data. Expansions in the assessed STR loci were successfully identified in WES and WGS datasets by all four methods with high specificity and sensitivity. Overall, exSTRa demonstrated more robust and superior performance for WES data than did the other three methods. We demonstrate that exSTRa can be effectively utilized as a screening tool for detecting repeat expansions in WES and WGS data, although the best performance would be produced by consensus calling, wherein at least two out of the four currently available screening methods call an expansion.
Collapse
Affiliation(s)
- Rick M Tankard
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne 3010, VIC, Australia; Mathematics and Statistics, Murdoch University, Murdoch 6150, WA, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne 3010, VIC, Australia; Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg 3084, VIC, Australia
| | - Peter Degorski
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne 3010, VIC, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville 3052, VIC, Australia; Victorian Clinical Genetics Services, Parkville 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville 3058, VIC, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville 3058, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville 3052, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne 3010, VIC, Australia.
| |
Collapse
|
47
|
Sedghi M, Salari M, Moslemi AR, Kariminejad A, Davis M, Goullée H, Olsson B, Laing N, Tajsharghi H. Ataxia-telangiectasia-like disorder in a family deficient for MRE11A, caused by a MRE11 variant. NEUROLOGY-GENETICS 2018; 4:e295. [PMID: 30584599 PMCID: PMC6283458 DOI: 10.1212/nxg.0000000000000295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022]
Abstract
Objective We report 3 siblings with the characteristic features of ataxia-telangiectasia-like disorder associated with a homozygous MRE11 synonymous variant causing nonsense-mediated mRNA decay (NMD) and MRE11A deficiency. Methods Clinical assessments, next-generation sequencing, transcript and immunohistochemistry analyses were performed. Results The patients presented with poor balance, developmental delay during the first year of age, and suffered from intellectual disability from early childhood. They showed oculomotor apraxia, slurred and explosive speech, limb and gait ataxia, exaggerated deep tendon reflex, dystonic posture, and mirror movement in their hands. They developed mild cognitive abilities. Brain MRI in the index case revealed cerebellar atrophy. Next-generation sequencing revealed a homozygous synonymous variant in MRE11 (c.657C>T, p.Asn219=) that we show affects splicing. A complete absence of MRE11 transcripts in the index case suggested NMD and immunohistochemistry confirmed the absence of a stable protein. Conclusions Despite the critical role of MRE11A in double-strand break repair and its contribution to the Mre11/Rad50/Nbs1 complex, the absence of MRE11A is compatible with life.
Collapse
Affiliation(s)
- Maryam Sedghi
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Mehri Salari
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Ali-Reza Moslemi
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Ariana Kariminejad
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Mark Davis
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Hayley Goullée
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Björn Olsson
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Nigel Laing
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| | - Homa Tajsharghi
- Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden
| |
Collapse
|
48
|
Exome sequencing in adult neurology practice: Challenges and rewards in a mixed resource setting. Clin Neurol Neurosurg 2018; 174:48-56. [DOI: 10.1016/j.clineuro.2018.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022]
|
49
|
Hurlimann T, Jaitovich Groisman I, Godard B. Exploring neurologists' perspectives on the return of next generation sequencing results to their patients: a needed step in the development of guidelines. BMC Med Ethics 2018; 19:81. [PMID: 30268121 PMCID: PMC6162934 DOI: 10.1186/s12910-018-0320-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background The use of Next Generation Sequencing such as Whole Genome Sequencing (WGS) is a promising step towards a better understanding and treatment of neurological diseases. WGS can result into unexpected information (incidental findings, IFs), and information with uncertain clinical significance. In the context of a Genome Canada project on ‘Personalized Medicine in the Treatment of Epilepsy’, we intended to address these challenges surveying neurologists’ opinions about the type of results that should be returned, and their professional responsibility toward recontacting patients regarding new discovered mutations. Methods Potential participants were contacted through professional organizations or direct invitations. Results A total of 204 neurologists were recruited. Fifty nine percent indicated that to be conveyed, WGS results should have a demonstrated clinical utility for diagnosis, prognosis or treatment. Yet, 41% deemed appropriate to return results without clinical utility, when they could impact patients’ reproductive decisions, or on patients’ request. Current use of targeted genetic testing and age of patients influenced respondents’ answers. Respondents stated that analysis of genomics data resulting from WGS should be limited to the genes likely to be relevant for the patient’s specific medical condition (69%), so as to limit IFs. Respondents felt responsible to recontact patients and inform them about newly discovered mutations related to the medical condition that triggered the test (75%) for as long as they are following up on the patient (55%). Finally, 53.5% of the respondents felt responsible to recontact and inform patients of clinically significant, newly discovered IFs. Conclusion Our results show the importance of formulating professional guidelines sensitive to the various – and sometimes opposite – viewpoints that may prevail within a same community of practice, as well as flexible so as to be attuned to the characteristics of the neurological conditions that triggered a WGS.
Collapse
Affiliation(s)
- Thierry Hurlimann
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Iris Jaitovich Groisman
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Béatrice Godard
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Department of Social and Preventive Medicine, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.
| |
Collapse
|
50
|
Wong MMK, Hoekstra SD, Vowles J, Watson LM, Fuller G, Németh AH, Cowley SA, Ansorge O, Talbot K, Becker EBE. Neurodegeneration in SCA14 is associated with increased PKCγ kinase activity, mislocalization and aggregation. Acta Neuropathol Commun 2018; 6:99. [PMID: 30249303 PMCID: PMC6151931 DOI: 10.1186/s40478-018-0600-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/30/2023] Open
Abstract
Spinocerebellar ataxia type 14 (SCA14) is a subtype of the autosomal dominant cerebellar ataxias that is characterized by slowly progressive cerebellar dysfunction and neurodegeneration. SCA14 is caused by mutations in the PRKCG gene, encoding protein kinase C gamma (PKCγ). Despite the identification of 40 distinct disease-causing mutations in PRKCG, the pathological mechanisms underlying SCA14 remain poorly understood. Here we report the molecular neuropathology of SCA14 in post-mortem cerebellum and in human patient-derived induced pluripotent stem cells (iPSCs) carrying two distinct SCA14 mutations in the C1 domain of PKCγ, H36R and H101Q. We show that endogenous expression of these mutations results in the cytoplasmic mislocalization and aggregation of PKCγ in both patient iPSCs and cerebellum. PKCγ aggregates were not efficiently targeted for degradation. Moreover, mutant PKCγ was found to be hyper-activated, resulting in increased substrate phosphorylation. Together, our findings demonstrate that a combination of both, loss-of-function and gain-of-function mechanisms are likely to underlie the pathogenesis of SCA14, caused by mutations in the C1 domain of PKCγ. Importantly, SCA14 patient iPSCs were found to accurately recapitulate pathological features observed in post-mortem SCA14 cerebellum, underscoring their potential as relevant disease models and their promise as future drug discovery tools.
Collapse
Affiliation(s)
- Maggie M. K. Wong
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Road, Oxford, OX1 3PT UK
| | - Stephanie D. Hoekstra
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Road, Oxford, OX1 3PT UK
| | - Jane Vowles
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Lauren M. Watson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Road, Oxford, OX1 3PT UK
| | - Geraint Fuller
- Gloucestershire Hospitals, NHS Foundation Trust, Cheltenham General Hospital, Sandford Road, Cheltenham, GL53 7AN UK
| | - Andrea H. Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford, OX3 9DU UK
- Oxford Centre for Genomic Medicine, ACE Building, Oxford University Hospitals NHS Trust, Nuffield Orthopaedic Centre, Windmill Road, Oxford, OX3 7HE UK
| | - Sally A. Cowley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford, OX3 9DU UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford, OX3 9DU UK
| | - Esther B. E. Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Road, Oxford, OX1 3PT UK
| |
Collapse
|