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Pegat A, Chanson JB, Lozeron P, Joubert B, Bani-Sadr A, Quadrio I, Vidoni L, Latour P. Identification of rare variants in the FBXO38 gene of patients with chronic inflammatory demyelinating polyradiculoneuropathy. J Neuroimmunol 2024; 392:578381. [PMID: 38823119 DOI: 10.1016/j.jneuroim.2024.578381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/13/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is a rare immune-mediated neuropathy for which there is no clearly identified risk factor. The present study identified rare variants in the FBXO38 gene in three familial cases of CIDP with response to corticosteroids in three generations with incomplete penetrance, and in an unrelated fourth case with diffuse nerve hypertrophy. FBXO38 may be involved in the regulation of the immunity mediated by CD8 T cells, which have an important role in CIDP pathophysiology, through PD1 degradation. Considering these findings, FBXO38 should be investigated as a potential genetic factor in larger cohorts of patients with CIDP.
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Affiliation(s)
- Antoine Pegat
- Service ENMG et de pathologies neuromusculaires, centre de référence des maladies neuromusculaires PACA-Réunion-Rhône Alpes, Hôpital Neurologique P. Wertheimer, Hospices Civils de Lyon, France.
| | - Jean-Baptiste Chanson
- Département de neurologie, Hôpitaux universitaire de Strasbourg et centre de référence neuromusculaire Nord/Est/Ile de France, Strasbourg, France
| | - Pierre Lozeron
- Service de Physiologie clinique-Explorations fonctionnelles, Hôpital Lariboisière, APHP, Paris, France
| | - Bastien Joubert
- Département de Neurologie, Hôpital Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Alexandre Bani-Sadr
- Département de Neuroradiologie, Hôpital Neurologique P. Wertheimer, Hospices Civils de Lyon, France
| | - Isabelle Quadrio
- Unité fonctionnelle de neurogénétique moléculaire, Groupement Hospitalier Est, Hospices Civils de Lyon, France
| | - Léo Vidoni
- Unité fonctionnelle de neurogénétique moléculaire, Groupement Hospitalier Est, Hospices Civils de Lyon, France
| | - Philippe Latour
- Unité fonctionnelle de neurogénétique moléculaire, Groupement Hospitalier Est, Hospices Civils de Lyon, France
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2
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Duraisamy AJ, Liu R, Sureshkumar S, Rose R, Jagannathan L, da Silva C, Coovadia A, Ramachander V, Chandrasekar S, Raja I, Sajnani M, Selvaraj SM, Narang B, Darvishi K, Bhayal AC, Katikala L, Guo F, Chen-Deutsch X, Balciuniene J, Ma Z, Nallamilli BRR, Bean L, Collins C, Hegde M. Focused Exome Sequencing Gives a High Diagnostic Yield in the Indian Subcontinent. J Mol Diagn 2024; 26:510-519. [PMID: 38582400 DOI: 10.1016/j.jmoldx.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/11/2023] [Accepted: 03/01/2024] [Indexed: 04/08/2024] Open
Abstract
The genetically isolated yet heterogeneous and highly consanguineous Indian population has shown a higher prevalence of rare genetic disorders. However, there is a significant socioeconomic burden for genetic testing to be accessible to the general population. In the current study, we analyzed next-generation sequencing data generated through focused exome sequencing from individuals with different phenotypic manifestations referred for genetic testing to achieve a molecular diagnosis. Pathogenic or likely pathogenic variants are reported in 280 of 833 cases with a diagnostic yield of 33.6%. Homozygous sequence and copy number variants were found as positive diagnostic findings in 131 cases (15.7%) because of the high consanguinity in the Indian population. No relevant findings related to reported phenotype were identified in 6.2% of the cases. Patients referred for testing due to metabolic disorder and neuromuscular disorder had higher diagnostic yields. Carrier testing of asymptomatic individuals with a family history of the disease, through focused exome sequencing, achieved positive diagnosis in 54 of 118 cases tested. Copy number variants were also found in trans with single-nucleotide variants and mitochondrial variants in a few of the cases. The diagnostic yield and the findings from this study signify that a focused exome test is a good lower-cost alternative for whole-exome and whole-genome sequencing and as a first-tier approach to genetic testing.
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Affiliation(s)
| | - Ruby Liu
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | - Rajiv Rose
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | - Indu Raja
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | | | - Fen Guo
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | | | | | | | - Lora Bean
- Revvity Omics, Pittsburgh, Pennsylvania
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3
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Gayed MM, Sgobbi P, Pinto WBVDR, Kishnani PS, Koch RL. Case report: Expanding the understanding of the adult polyglucosan body disease continuum: novel presentations, diagnostic pitfalls, and clinical pearls. Front Genet 2023; 14:1282790. [PMID: 38164512 PMCID: PMC10758020 DOI: 10.3389/fgene.2023.1282790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Adult polyglucosan body disease (APBD) has long been regarded as the adult-onset form of glycogen storage disease type IV (GSD IV) and is caused by biallelic pathogenic variants in GBE1. Advances in the understanding of the natural history of APBD published in recent years have led to the use of discrete descriptors ("typical" versus "atypical") based on adherence to traditional symptomatology and homozygosity for the p.Y329S variant. Although these general descriptors are helpful in summarizing common findings and symptoms in APBD, they are inherently limited and may affect disease recognition in diverse populations. Methods: This case series includes three American patients (cases 1-3) and four Brazilian patients (cases 4-7) diagnosed with APBD. Patient-reported outcome (PRO) measures were employed to evaluate pain, fatigue, and quality of life in cases 1-3. Results: We describe the clinical course and diagnostic odyssey of seven cases of APBD that challenge the utility and efficacy of discrete descriptors. Cases 1-3 are compound heterozygotes that harbor the previously identified deep intronic variant in GBE1 and presented with "typical" APBD phenotypically, despite lacking two copies of the pathogenic p.Y329S variant. Patient-reported outcome measures in these three cases revealed the moderate levels of pain and fatigue as well as an impacted quality of life. Cases 4-7 have unique genotypic profiles and emphasize the growing recognition of presentations of APBD in diverse populations with broad neurological manifestations. Conclusion: Collectively, these cases underscore the understanding of APBD as a spectrum disorder existing on the GSD IV phenotypic continuum. We draw attention to the pitfalls of commonly used genetic testing methods when diagnosing APBD and highlight the utility of patient-reported outcome questionnaires in managing this disease.
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Affiliation(s)
- Matthew M. Gayed
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Paulo Sgobbi
- Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, University of São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Priya S. Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Rebecca L. Koch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
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Triono A, Iskandar K, Hadiyanto ML, Nugrahanto AP, Diantika K, Wijayanti VW, Herini ES. Identification of the genetic basis of pediatric neurogenetic disorders at a tertiary referral hospital in Indonesia: Contribution of whole exome sequencing. PLoS One 2023; 18:e0293113. [PMID: 37878632 PMCID: PMC10599538 DOI: 10.1371/journal.pone.0293113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Neurogenetic disorders (NGDs) are complex Mendelian disorders that affect the neurological system. A molecular diagnosis will provide more information about pathophysiology, prognosis, and therapy, including future genetic therapy options. Whole-Exome Sequencing (WES) can rapidly discover the genetic basis in NGDs. OBJECTIVE The purpose of this study was to assess the WES results and its value in diagnosing pediatric NGDs, especially those with unspecified clinical features. METHODS A retrospective chart review was performed from May 2021- February 2023 in Dr. Sardjito General Hospital, a tertiary referral hospital in Yogyakarta, Indonesia. WES proband only was conducted on children aged 0 to 17 years old who met one or more of the following criteria: (1) epileptic encephalopathy and familial epilepsy; (2) complex neurodevelopmental phenotypes; (3) leukodystrophy; (4) movement disorders; and (5) neurocutaneous disorder. The WES was conducted in the certified laboratory, 3Billion, in Seoul, Korea. RESULTS The diagnosis yield of WES in our study was 45% (9/20). We identified nine positive results, including eight pathogenic single nucleotide variants (SNVs) in 8 genes (KCNQ2, ARSA, UBE3A, IRF2BPL, ATM, MECP2, TSC2, and NF1), and one variant with uncertain significance (VUS) in the ADK gene that has not been able to explain the observed clinical features. Of the nine patients with positive WES results, five had missense mutations, three frameshift mutations, and one nonsense mutation. Additionally, we identified two suggestive copy number variants (CNVs) in 15q11.2q13.1 and 1p31.3. CONCLUSIONS Whole-Exome Sequencing is an essential diagnostic tool for pediatric NGDs, especially those with unspecified clinical features. It ends multi-year diagnostic odysseys, provides personalized medicine therapy, and optimizes genetic counselling for these families.
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Affiliation(s)
- Agung Triono
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Academic UGM Hospital, Yogyakarta, Indonesia
| | - Marissa Leviani Hadiyanto
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Andika Priamas Nugrahanto
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kania Diantika
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Veronica Wulan Wijayanti
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Elisabeth Siti Herini
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, Indonesia
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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6
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Marinella G, Orsini A, Scacciati M, Costa E, Santangelo A, Astrea G, Frosini S, Pasquariello R, Rubegni A, Sgherri G, Corsi M, Bonuccelli A, Battini R. Congenital Myopathy as a Phenotypic Expression of CACNA1S Gene Mutation: Case Report and Systematic Review of the Literature. Genes (Basel) 2023; 14:1363. [PMID: 37510268 PMCID: PMC10379235 DOI: 10.3390/genes14071363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Congenital myopathies are a group of clinically, genetically, and histologically heterogeneous diseases caused by mutations in a large group of genes. One of these is CACNA1S, which is recognized as the cause of Dihydropyridine Receptor Congenital Myopathy. METHODS To better characterize the phenotypic spectrum of CACNA1S myopathy, we conducted a systematic review of cases in the literature through three electronic databases following the PRISMA guidelines. We selected nine articles describing 23 patients with heterozygous, homozygous, or compound heterozygous mutations in CACNA1S and we added one patient with a compound heterozygous mutation in CACNA1S (c.1394-2A>G; c.1724T>C, p.L575P) followed at our Institute. We collected clinical and genetic data, muscle biopsies, and muscle MRIs when available. RESULTS The phenotype of this myopathy is heterogeneous, ranging from more severe forms with a lethal early onset and mild-moderate forms with a better clinical course. CONCLUSIONS Our patient presented a phenotype compatible with the mild-moderate form, although she presented peculiar features such as a short stature, myopia, mild sensorineural hearing loss, psychiatric symptoms, and posterior-anterior impairment gradient on thigh muscle MRI.
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Affiliation(s)
- Gemma Marinella
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Alessandro Orsini
- Pediatric Neurology, Pediatric University Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56100 Pisa, Italy; (A.O.); (M.S.); (A.S.); (A.B.)
| | - Massimo Scacciati
- Pediatric Neurology, Pediatric University Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56100 Pisa, Italy; (A.O.); (M.S.); (A.S.); (A.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Elisa Costa
- Pediatric Neurology, Pediatric University Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56100 Pisa, Italy; (A.O.); (M.S.); (A.S.); (A.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Andrea Santangelo
- Pediatric Neurology, Pediatric University Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56100 Pisa, Italy; (A.O.); (M.S.); (A.S.); (A.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Guja Astrea
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Silvia Frosini
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Rosa Pasquariello
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Anna Rubegni
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Giada Sgherri
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
| | - Martina Corsi
- Department of Preventive and Occupational Medicine, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56126 Pisa, Italy;
| | - Alice Bonuccelli
- Pediatric Neurology, Pediatric University Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56100 Pisa, Italy; (A.O.); (M.S.); (A.S.); (A.B.)
| | - Roberta Battini
- Department of Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (G.M.); (G.A.); (S.F.); (R.P.); (A.R.); (G.S.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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7
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Koch RL, Soler-Alfonso C, Kiely BT, Asai A, Smith AL, Bali DS, Kang PB, Landstrom AP, Akman HO, Burrow TA, Orthmann-Murphy JL, Goldman DS, Pendyal S, El-Gharbawy AH, Austin SL, Case LE, Schiffmann R, Hirano M, Kishnani PS. Diagnosis and management of glycogen storage disease type IV, including adult polyglucosan body disease: A clinical practice resource. Mol Genet Metab 2023; 138:107525. [PMID: 36796138 DOI: 10.1016/j.ymgme.2023.107525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Glycogen storage disease type IV (GSD IV) is an ultra-rare autosomal recessive disorder caused by pathogenic variants in GBE1 which results in reduced or deficient glycogen branching enzyme activity. Consequently, glycogen synthesis is impaired and leads to accumulation of poorly branched glycogen known as polyglucosan. GSD IV is characterized by a remarkable degree of phenotypic heterogeneity with presentations in utero, during infancy, early childhood, adolescence, or middle to late adulthood. The clinical continuum encompasses hepatic, cardiac, muscular, and neurologic manifestations that range in severity. The adult-onset form of GSD IV, referred to as adult polyglucosan body disease (APBD), is a neurodegenerative disease characterized by neurogenic bladder, spastic paraparesis, and peripheral neuropathy. There are currently no consensus guidelines for the diagnosis and management of these patients, resulting in high rates of misdiagnosis, delayed diagnosis, and lack of standardized clinical care. To address this, a group of experts from the United States developed a set of recommendations for the diagnosis and management of all clinical phenotypes of GSD IV, including APBD, to support clinicians and caregivers who provide long-term care for individuals with GSD IV. The educational resource includes practical steps to confirm a GSD IV diagnosis and best practices for medical management, including (a) imaging of the liver, heart, skeletal muscle, brain, and spine, (b) functional and neuromusculoskeletal assessments, (c) laboratory investigations, (d) liver and heart transplantation, and (e) long-term follow-up care. Remaining knowledge gaps are detailed to emphasize areas for improvement and future research.
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Affiliation(s)
- Rebecca L Koch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
| | - Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bridget T Kiely
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Akihiro Asai
- Department of Pediatrics, University of Cincinnati Medical Center, Cincinnati, OH, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ariana L Smith
- Division of Urology, Department of Surgery, University of Pennsylvania Health System, Philadelphia, PA, USA
| | - Deeksha S Bali
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Peter B Kang
- Paul and Sheila Wellstone Muscular Dystrophy Center, Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Andrew P Landstrom
- Division of Cardiology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA; Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - H Orhan Akman
- Department of Neurology, Columbia University Irving Medical Center, New York City, NY, USA
| | - T Andrew Burrow
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | | | - Deberah S Goldman
- Adult Polyglucosan Body Disease Research Foundation, Brooklyn, NY, USA
| | - Surekha Pendyal
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Areeg H El-Gharbawy
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Stephanie L Austin
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Laura E Case
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA; Doctor of Physical Therapy Division, Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York City, NY, USA
| | - Priya S Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
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8
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Oh SJ, King PH, Schindler A. Life-Long Steroid Responsive Familial Myopathy With Docking Protein 7 Mutation. J Clin Neuromuscul Dis 2022; 24:80-84. [PMID: 36409338 DOI: 10.1097/cnd.0000000000000398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Docking protein 7 (DOK7) congenital myasthenic syndrome (CMS) is characterized by limb-girdle weakness and lack of fluctuating fatigability simulating many familial myopathies. Albuterol is the first line of therapy in view of consistent improvement. Two brothers with progressive predominant biceps weakness for 1-3 years responded to prednisone treatment for 40-50 years. Various studies including muscle biopsy and many laboratory studies were unsuccessful for the definite diagnosis. Gene study, 40 years after the initial evaluation, confirmed the diagnosis of DOK7 CMS. These are the first reported cases of DOK7 CMS associated with a sustained benefit from corticosteroids.
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Affiliation(s)
- Shin J Oh
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL; and
| | - Peter H King
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL; and
| | - Alice Schindler
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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9
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Khan A, Tian S, Tariq M, Khan S, Safeer M, Ullah N, Akbar N, Javed I, Asif M, Ahmad I, Ullah S, Satti HS, Khan R, Naeem M, Ali M, Rendu J, Fauré J, Dieterich K, Latypova X, Baig SM, Malik NA, Zhang F, Khan TN, Liu C. NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes. Mol Genet Genomics 2022; 297:1601-1613. [PMID: 36002593 DOI: 10.1007/s00438-022-01945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
Hereditary neurological disorders (HNDs) are a clinically and genetically heterogeneous group of disorders. These disorders arise from the impaired function of the central or peripheral nervous system due to aberrant electrical impulses. More than 600 various neurological disorders, exhibiting a wide spectrum of overlapping clinical presentations depending on the organ(s) involved, have been documented. Owing to this clinical heterogeneity, diagnosing these disorders has been a challenge for both clinicians and geneticists and a large number of patients are either misdiagnosed or remain entirely undiagnosed. Contribution of genetics to neurological disorders has been recognized since long; however, the complete picture of the underlying molecular bases are under-explored. The aim of this study was to accurately diagnose 11 unrelated Pakistani families with various HNDs deploying NGS as a first step approach. Using exome sequencing and gene panel sequencing, we successfully identified disease-causing genomic variants these families. We report four novel variants, one each in, ECEL1, NALCN, TBR1 and PIGP in four of the pedigrees. In the rest of the seven families, we found five previously reported pathogenic variants in POGZ, FA2H, PLA2G6 and CYP27A1. Of these, three families segregate a homozygous 18 bp in-frame deletion of FA2H, indicating a likely founder mutation segregating in Pakistani population. Genotyping for this mutation can help low-cost population wide screening in the corresponding regions of the country. Our findings not only expand the existing repertoire of mutational spectrum underlying neurological disorders but will also help in genetic testing of individuals with HNDs in other populations.
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Affiliation(s)
- Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Shixiong Tian
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Safeer
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Naimat Ullah
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Nazia Akbar
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Iram Javed
- Department of Paediatric Neurology, Children Hospital and Institute of Child Health, Faisalabad, Pakistan
| | - Mahnoor Asif
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Ilyas Ahmad
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck, Germany
| | - Shahid Ullah
- Department of General Surgery, Hayatabad Medical Complex, Peshawar, 2500, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - John Rendu
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Julien Fauré
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Klaus Dieterich
- Inserm, U1209, CHU Grenoble Alpes, Institute of Advanced Biosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Xenia Latypova
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Shahid Mahmood Baig
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan
| | - Naveed Altaf Malik
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China
| | - Tahir Naeem Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States.
| | - Chunyu Liu
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China.
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10
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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