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Morales-Romero B, Muñoz-Pujol G, Artuch R, García-Cazorla A, O'Callaghan M, Sykut-Cegielska J, Campistol J, Moreno-Lozano PJ, Oud MM, Wevers RA, Lefeber DJ, Esteve-Codina A, Yepez VA, Gagneur J, Wortmann SB, Prokisch H, Ribes A, García-Villoria J, Tort F. Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing. Mol Genet Metab 2024; 142:108511. [PMID: 38878498 DOI: 10.1016/j.ymgme.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
The diagnosis of Mendelian disorders has notably advanced with integration of whole exome and genome sequencing (WES and WGS) in clinical practice. However, challenges in variant interpretation and uncovered variants by WES still leave a substantial percentage of patients undiagnosed. In this context, integrating RNA sequencing (RNA-seq) improves diagnostic workflows, particularly for WES inconclusive cases. Additionally, functional studies are often necessary to elucidate the impact of prioritized variants on gene expression and protein function. Our study focused on three unrelated male patients (P1-P3) with ATP6AP1-CDG (congenital disorder of glycosylation), presenting with intellectual disability and varying degrees of hepatopathy, glycosylation defects, and an initially inconclusive diagnosis through WES. Subsequent RNA-seq was pivotal in identifying the underlying genetic causes in P1 and P2, detecting ATP6AP1 underexpression and aberrant splicing. Molecular studies in fibroblasts confirmed these findings and identified the rare intronic variants c.289-233C > T and c.289-289G > A in P1 and P2, respectively. Trio-WGS also revealed the variant c.289-289G > A in P3, which was a de novo change in both patients. Functional assays expressing the mutant alleles in HAP1 cells demonstrated the pathogenic impact of these variants by reproducing the splicing alterations observed in patients. Our study underscores the role of RNA-seq and WGS in enhancing diagnostic rates for genetic diseases such as CDG, providing new insights into ATP6AP1-CDG molecular bases by identifying the first two deep intronic variants in this X-linked gene. Additionally, our study highlights the need to integrate RNA-seq and WGS, followed by functional validation, in routine diagnostics for a comprehensive evaluation of patients with an unidentified molecular etiology.
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Affiliation(s)
- Blai Morales-Romero
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, CIBERER, Esplugues de Llobregat, Barcelona, Spain.
| | - Angels García-Cazorla
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Mar O'Callaghan
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Pediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Jaume Campistol
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Pedro Juan Moreno-Lozano
- Inherited Metabolic Diseases and Muscle Disorders' Research Group, Department of Internal Medicine, Hospital Clinic de Barcelona, IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Ron A Wevers
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Dirk J Lefeber
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain.
| | - Vicente A Yepez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Saskia B Wortmann
- University Children's Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria; Amalia Children's Hospital, Department of Pediatrics, Radboudumc, Nijmegen, the Netherlands.
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Judit García-Villoria
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
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Kerkhof J, Rastin C, Levy MA, Relator R, McConkey H, Demain L, Dominguez-Garrido E, Kaat LD, Houge SD, DuPont BR, Fee T, Fletcher RS, Gokhale D, Haukanes BI, Henneman P, Hilton S, Hilton BA, Jenkinson S, Lee JA, Louie RJ, Motazacker MM, Rzasa J, Stevenson RE, Plomp A, van der Laan L, van der Smagt J, Walden KK, Banka S, Mannens M, Skinner SA, Friez MJ, Campbell C, Tedder ML, Alders M, Sadikovic B. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med 2024; 26:101075. [PMID: 38251460 DOI: 10.1016/j.gim.2024.101075] [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: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
PURPOSE This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
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Affiliation(s)
- Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sofia Douzgou Houge
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | | | | | | | - David Gokhale
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Bjørn Ivar Haukanes
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - M Mahdi Motazacker
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Astrid Plomp
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jasper van der Smagt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Marcel Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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4
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Ancora C, Marchi M, Bonardi CM, Sartori G, Lopreiato R, Zuccarello D, D'Errico I, Nosadini M, Sartori S, Boniver C, Toldo I, Salviati L. Electroclinical Features in Two Novel STRADA Patients and a Functional Yeast Assay for the Validation of Missense STRADA Mutations. Pediatr Neurol 2023; 148:152-156. [PMID: 37722301 DOI: 10.1016/j.pediatrneurol.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/20/2023]
Abstract
Loss of function of the STRADA gene, an upstream mTOR inhibitor, causes a rare neurodevelopmental disorder characterized by polyhydramnios, megalencephaly, and symptomatic epilepsy (PMSE syndrome). Patients display a homogeneous phenotype including early-onset drug-resistant epilepsy, severe psychomotor delay, multisystemic comorbidities, and increased risk of premature death. The administration of sirolimus, an mTOR inhibitor, is helpful in controlling seizures in this syndrome. We report the electroclinical phenotype of two novel patients and the development of a yeast model to validate the pathogenicity of missense variants. Patient 1 harbored a missense STRADA variant and had a peculiar electroclinical phenotype with a relatively mild epilepsy course. Patient 2 harbored a truncating STRADA variant and showed a typical PMSE phenotype and a favorable response to early treatment with sirolimus. When we modeled the p.(Ser264Arg) STRADA change in its yeast homolog SPS1, it impaired SPS1 function. The results underlie the importance of a timely molecular diagnosis in these patients and show that yeast is a simple yet effective model to validate the pathogenicity of missense variants.
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Affiliation(s)
- Caterina Ancora
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Marco Marchi
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy; Clinical Genetics Lab, Città della Speranza Pediatric Research Institute, Padua, Italy
| | - Claudia Maria Bonardi
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | | | - Daniela Zuccarello
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | | | - Margherita Nosadini
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Stefano Sartori
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Clementina Boniver
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Irene Toldo
- Pediatric Neurology and Neurophysiology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy.
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy; Clinical Genetics Lab, Città della Speranza Pediatric Research Institute, Padua, Italy
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Li N, Kang H, Zou Y, Liu Z, Deng Y, Wang M, Li L, Qin H, Qiu X, Wang Y, Zhu J, Agostino M, Heng JIT, Yu P. A novel heterozygous ZBTB18 missense mutation in a family with non-syndromic intellectual disability. Neurogenetics 2023; 24:251-262. [PMID: 37525067 DOI: 10.1007/s10048-023-00727-7] [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: 05/04/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Intellectual disability (ID) is a common neurodevelopmental disorder characterized by significantly impaired adaptive behavior and cognitive capacity. High throughput sequencing approaches have revealed the genetic etiologies for 25-50% of ID patients, while inherited genetic mutations were detected in <5% cases. Here, we investigated the genetic cause for non-syndromic ID in a Han Chinese family. Whole genome sequencing was performed on identical twin sisters diagnosed with ID, their respective children, and their asymptomatic parents. Data was filtered for rare variants, and in silico prediction tools were used to establish pathogenic alleles. Candidate mutations were validated by Sanger sequencing. In silico modeling was used to evaluate the mutation's effects on the protein encoded by a candidate coding gene. A novel heterozygous variant in the ZBTB18 gene c.1323C>G (p.His441Gln) was identified. This variant co-segregated with affected individuals in an autosomal dominant pattern and was not detected in asymptomatic family members. Molecular studies reveal that a p.His441Gln substitution disrupts zinc binding within the second zinc finger and disrupts the capacity for ZBTB18 to bind DNA. This is the first report of an inherited ZBTB18 mutation for ID. This study further validates WGS for the accurate molecular diagnosis of ID.
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Affiliation(s)
- Nana Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Hong Kang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Yanna Zou
- Department of Gynaecology and Obstetrics, Changyi Maternal and Child Care Hospital, Weifang, Shandong, China
| | - Zhen Liu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Ying Deng
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Meixian Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Lu Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Hong Qin
- Department of Gynaecology and Obstetrics, Wuhou District People's Hospital, Chengdu, Sichuan, China
| | - Xiaoqiong Qiu
- Department of Obstetrics and Gynecology, Pidu District People's Hospital, Chengdu, China
| | - Yanping Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Mark Agostino
- Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Australia
- Curtin Medical School, Curtin University, Bentley, Australia
| | - Julian I-T Heng
- Faculty of Health Sciences, Curtin University, Bentley, Australia.
| | - Ping Yu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China.
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Cole JJ, Sellitto AD, Baratta LR, Huecker JB, Balls-Berry JE, Gurnett CA. Social Determinants of Genetics Referral and Completion Rates Among Child Neurology Patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295450. [PMID: 37745339 PMCID: PMC10516043 DOI: 10.1101/2023.09.12.23295450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Objective To investigate clinical, social, and systems-level determinants predictive of genetics clinic referral and completion of genetics clinic visits among child neurology patients. Methods Electronic health record data were extracted from patients 0-18 years old who were evaluated in child neurology clinics at a single tertiary care institution between July 2018 to January 2020. Variables aligned with the Health Equity Implementation Framework. Referral and referral completion rates to genetics and cardiology clinics were compared among Black vs White patients using bivariate analysis. Demographic variables associated with genetics clinic referral and visit completion were identified using logistic regressions. Results In a cohort of 11,371 child neurology patients, 304 genetics clinic referrals and 82 cardiology clinic referrals were placed. In multivariate analysis of patients with Black or White ethnoracial identity (n=10,601), genetics clinic referral rates did not differ by race, but were significantly associated with younger age, rural address, neurodevelopmental disorder diagnosis, number of neurology clinic visits, and provider type. The only predictors of genetics clinic visit completion number of neurology clinic visits and race/ethnicity, with White patients being twice as likely as Black patients to complete the visit. Cardiology clinic referrals and visit completion did not differ by race/ethnicity. Interpretation Although race/ethnicity was not associated with differences in genetics clinic referral rates, White patients were twice as likely as Black patients to complete a genetics clinic visit after referral. Further work is needed to determine whether this is due to systemic/structural racism, differences in attitudes toward genetic testing, or other factors.
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Affiliation(s)
- Jordan J Cole
- Washington University in St. Louis, Department of Neurology
- University of Colorado, Department of Pediatrics
| | | | | | - Julia B Huecker
- Washington University in St. Louis, Center for Biostatistics & Data Science
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Pinto WBVDR, Oliveira ASB, Carvalho AADS, Akman HO, de Souza PVS. Editorial: The expanding clinical and genetic basis of adult inherited neurometabolic disorders. Front Neurol 2023; 14:1255513. [PMID: 37560451 PMCID: PMC10408293 DOI: 10.3389/fneur.2023.1255513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023] Open
Affiliation(s)
- Wladimir Bocca Vieira de Rezende Pinto
- Division of Neuromuscular Diseases, Neurometabolic Unit, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Acary Souza Bulle Oliveira
- Division of Neuromuscular Diseases, Neurometabolic Unit, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | | | | | - Paulo Victor Sgobbi de Souza
- Division of Neuromuscular Diseases, Neurometabolic Unit, Department of Neurology and Neurosurgery, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
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8
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Tein I. Recent advances in neurometabolic diseases: The genetic role in the modern era. Epilepsy Behav 2023; 145:109338. [PMID: 37453291 DOI: 10.1016/j.yebeh.2023.109338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
The global birth prevalence of all inborn errors of metabolism (IEMs) in children (49 studies, 1980-2017) is approximately 50.9/100,000 live births. Regional pooled birth prevalence showed higher rates in Eastern Mediterranean regions (75.7/100,000 live births) and highest in Saudi Arabia (169/100,000) with higher parental consanguinity rates of ∼60%. Case fatality rates globally are estimated to be 33% or higher. IEMs are a group of >600 heterogeneous disorders often presenting in newborns and infants with drug-resistant seizures and/or encephalopathy. Early diagnosis and treatments are key in the prevention of morbidity, early mortality, and high lifetime health care costs, such as the early recognition of the newborn with pyridoxine- or pyridoxal-L-phosphate-dependent seizures which do not respond to standard antiepileptic drugs. The earlier the recognition and intervention in the specific cofactor- or vitamin-responsive epilepsies, the better the outcome and prevention of intractable seizures and encephalopathy leading to irreversible neurologic injury. In recent years, the genetics of IEMs has been transformed by the emergence of new molecular genetic technologies. Depending upon the clinical phenotype, current genetic testing may include chromosomal microarray (deletion/duplication analysis), single target gene sequencing, gene panels (sequencing and deletion/duplication analysis), DNA methylation analysis, mitochondrial nuclear gene panel, and mtDNA sequencing and/or trio WES or WGS (which have reduced in costs). A meta-analysis, showed WES and epilepsy gene panels to be the most cost-effective genetic tests for unknown epilepsies versus chromosomal microarray. Most recently, rapid genomic sequencing (RGS) has been associated with a shorter time to diagnosis (3 days) and increased diagnostic yield when compared with standard-of-care testing, including gene panels and microarrays. A randomized controlled trial (RCT) of rapid(r) WGS or rWES in acutely ill infants with diseases of unknown etiology in pediatric ICUs in San Diego, California found RGS to be highly clinically useful for 77% of 201 infants. RGS changed clinical management in 28% of infants and outcomes in 15%. An Australian study of ultra-rapid (ur) exome sequencing (mean time to genomic test report of 3.3 days) in 108 critically ill infants and children with suspected monogenic conditions, had a molecular diagnostic yield of 51% with 20% requiring further genetic analysis. In 42/55 (76%), ur exome sequencing was felt to have influenced clinical management for targeted treatments, surveillance, or palliative care, however, the study was not designed or powered to measure differences in major clinical outcomes compared to standard care of critically ill patients. Further research is needed to understand this tool's clinical value and generalizability balanced against its high costs. A paradigm shift is evolving from pattern- and evidence-based medicine toward algorithm-based, precision medicine targeted to individual mutations. Meticulous clinical phenotyping and pedigree analysis, combined with advances in high-throughput metabolomics, proteomics, transcriptomics (RNAseq in clinically relevant tissues), and genomics, have expedited the identification of novel pathomechanisms and new therapeutic targets. Evaluation of these therapies in IEMs, many of which manifest with encephalopathy and epilepsy, will depend on international registries of well-characterized phenotypes in RCTs and measurement of clinically relevant endpoints. The earlier the recognition and diagnosis and intervention with targeted therapies, the better the overall outcome in terms of the impact on intellectual disability and the effective management of the associated epilepsy.
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Affiliation(s)
- Ingrid Tein
- Division of Neurology, Dept. of Pediatrics and Dept. of Laboratory Medicine and Pathobiology, The Genetics and Genome Biology Program, The Research Institute, The Hospital for Sick Children, The University of Toronto, Toronto, Ontario, Canada M5G 1X8.
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9
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Dai H, Zhu W, Yuan B, Walley N, Schoch K, Jiang YH, Phillips JA, Jones MS, Liu P, Murdock DR, Burrage LC, Lee B, Rosenfeld JA, Xiao R. A recurrent single-exon deletion in TBCK might be under-recognized in patients with infantile hypotonia and psychomotor delay. Hum Mutat 2022; 43:1816-1823. [PMID: 36317458 PMCID: PMC9772143 DOI: 10.1002/humu.24497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/08/2022]
Abstract
Advanced bioinformatics algorithms allow detection of multiple-exon copy-number variations (CNVs) from exome sequencing (ES) data, while detection of single-exon CNVs remains challenging. A retrospective review of Baylor Genetics' clinical ES patient cohort identified four individuals with homozygous single-exon deletions of TBCK (exon 23, NM_001163435.2), a gene associated with an autosomal recessive neurodevelopmental phenotype. To evaluate the prevalence of this deletion and its contribution to disease, we retrospectively analyzed single nucleotide polymorphism (SNP) array data for 8194 individuals undergoing ES, followed by PCR confirmation and RT-PCR on individuals carrying homozygous or heterozygous exon 23 TBCK deletions. A fifth individual was diagnosed with the TBCK-related disorder due to a heterozygous exon 23 deletion in trans with a c.1860+1G>A (NM_001163435.2) pathogenic variant, and three additional heterozygous carriers were identified. Affected individuals and carriers were from diverse ethnicities including European Caucasian, South Asian, Middle Eastern, Hispanic American and African American, with only one family reporting consanguinity. RT-PCR revealed two out-of-frame transcripts related to the exon 23 deletion. Our results highlight the importance of identifying single-exon deletions in clinical ES, especially for genes carrying recurrent deletions. For patients with early-onset hypotonia and psychomotor delay, this single-exon TBCK deletion might be under-recognized due to technical limitations of ES.
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Affiliation(s)
- Hongzheng Dai
- Molecular and Human Genetics, Baylor College of Medicine
- Molecular Genomics, Baylor Genetics
| | | | - Bo Yuan
- Molecular and Human Genetics, Baylor College of Medicine
- Molecular Genomics, Baylor Genetics
| | | | | | | | - John A. Phillips
- Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine
| | | | - Pengfei Liu
- Molecular and Human Genetics, Baylor College of Medicine
- Molecular Genomics, Baylor Genetics
| | | | - Lindsay C. Burrage
- Molecular and Human Genetics, Baylor College of Medicine
- Texas Children’s Hospital
| | - Brendan Lee
- Molecular and Human Genetics, Baylor College of Medicine
| | | | - Rui Xiao
- Molecular and Human Genetics, Baylor College of Medicine
- Molecular Genomics, Baylor Genetics
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11
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Goetz M, Schröter J, Dattner T, Brennenstuhl H, Lenz D, Opladen T, Hörster F, Okun JG, Hoffmann GF, Kölker S, Staufner C. Genotypic and phenotypic spectrum of cytosolic phosphoenolpyruvate carboxykinase deficiency. Mol Genet Metab 2022; 137:18-25. [PMID: 35868242 DOI: 10.1016/j.ymgme.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVES Pathogenic biallelic variants in PCK1 coding for the cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) cause PEPCK-C deficiency, a rare disorder of gluconeogenesis presenting with hypoglycemia, lactic acidosis, and hepatopathy. To date, there has been no systematic analysis of its phenotypic, biochemical, and genetic spectrum. METHODS All currently published individuals and a novel patient with genetically confirmed PEPCK-C deficiency were included. Clinical, biochemical, and genetic findings were analyzed. Protein and in-silico prediction score modeling was applied to analyze potential variant effects. RESULTS Thirty-two individuals from 25 families were found, including one previously unreported patient. The typical biochemical pattern was hypoglycemia triggered by catabolic situations, elevated urinary concentrations of tricarboxylic acid cycle metabolites, mildly elevated alanine and aspartate aminotransferase and elevated lactate concentrations in serum. Plasma glutamine concentrations were elevated in some patients and may be a suitable marker for newborn screening. With adequate treatment, biochemical abnormalities usually normalized following a hypoglycemic episode. Symptom onset usually occurred in infancy with a broad range from neonatal age to adulthood. Regardless of the genotype, different phenotypes with a broad clinical spectrum were found. To date, eight genotypes with nine different PCK1 variants were identified, of which alleles with the recurrent variant c.925G > A; p.(Gly309Arg) are predominant and appear to be endemic in the Finnish population. Protein modeling suggests altered manganese- and substrate-binding as superordinate pathomechanisms. CONCLUSIONS Environmental factors appear to be the main determinant for the phenotype in patients with biallelic variants in PCK1. Based on the biochemical pattern, PEPCK-C deficiency is a recognizable cause of childhood hypoglycemia. It is a treatable disease and early diagnosis is important to prevent metabolic derailment and morbidity. Newborn screening can identify at least a sub-cohort of affected individuals through elevated glutamine concentrations in dry blood.
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Affiliation(s)
- M Goetz
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - J Schröter
- Division of Pediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - T Dattner
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - H Brennenstuhl
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - D Lenz
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - T Opladen
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - F Hörster
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - J G Okun
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - G F Hoffmann
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - S Kölker
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - C Staufner
- Division of Child Neurology and Metabolic Disorders, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany..
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12
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Wang Q, Tang X, Yang K, Huo X, Zhang H, Ding K, Liao S. Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders. Mol Genet Genomic Med 2022; 10:e1918. [PMID: 35266334 PMCID: PMC9034680 DOI: 10.1002/mgg3.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Background Neurodevelopmental disorders, a group of early‐onset neurological disorders with significant clinical and genetic heterogeneity, remain a diagnostic challenge for clinical genetic evaluation. Therefore, we assessed the diagnostic yield by combining standard phenotypes and whole‐exome sequencing in families with these disorders that were “not yet diagnosed” by the traditional testing methods. Methods Using a standardized vocabulary of phenotypic abnormalities from human phenotype ontology (HPO), we performed deep phenotyping for 45 “not yet diagnosed” pedigrees to characterize multiple clinical features extracted from Chinese electronic medical records (EMRs). By matching HPO terms with known human diseases and phenotypes from model organisms, together with whole‐exome sequencing data, we prioritized candidate mutations/genes. We made probable genetic diagnoses for the families. Results We obtained a diagnostic yield of 29% (13 out of 45) with probably genetic diagnosis, of which compound heterozygosity and de novo mutations accounted for 77% (10/13) of the diagnosis. Of note, these pedigrees are accompanied by a more significant number of non‐neurological features. Conclusions Deep phenotyping and whole‐exome sequencing improve the etiological evaluation for neurodevelopmental disorders in the clinical setting.
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Affiliation(s)
- Qingqing Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xia Tang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Ke Yang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xiaodong Huo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Hui Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
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13
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Li D, Mukhopadhyay S. A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2. J Biol Chem 2021; 297:101069. [PMID: 34384782 PMCID: PMC8411240 DOI: 10.1016/j.jbc.2021.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 10/25/2022] Open
Abstract
The CMP-sialic acid transporter SLC35A1 and UDP-galactose transporter SLC35A2 are two well-characterized nucleotide sugar transporters with distinctive substrate specificities. Mutations in either induce congenital disorders of glycosylation. Despite the biomedical relevance, mechanisms of substrate specificity are unclear. To address this critical issue, we utilized a structure-guided mutagenesis strategy and assayed a series of SLC35A2 and SLC35A1 mutants using a rescue approach. Our results suggest that three pockets in the central cavity of each transporter provide substrate specificity. The pockets comprise (1) nucleobase (residues E52, K55, and Y214 of SLC35A1; E75, K78, N235, and G239 of SLC35A2); (2) middle (residues Q101, N102, and T260 of SLC35A1; Q125, N126, Q129, Y130, and Q278 of SLC35A2); and (3) sugar (residues K124, T128, S188, and K272 of SLC35A1; K148, T152, S213, and K297 of SLC35A2) pockets. Within these pockets, two components appear to be especially critical for substrate specificity. Y214 (for SLC35A1) and G239 (for SLC35A2) in the nucleobase pocket appear to discriminate cytosine from uracil. Furthermore, Q129 and Q278 of SLC35A2 in the middle pocket appear to interact specifically with the β-phosphate of UDP while the corresponding A105 and A253 residues in SLC35A1 do not interact with CMP, which lacks a β-phosphate. Overall, our findings contribute to a molecular understanding of substrate specificity and coordination in SLC35A1 and SLC35A2, and have important implications for the understanding and treatment of diseases associated with mutations or dysregulations of these two transporters.
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Affiliation(s)
- Danyang Li
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712.
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14
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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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15
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Abuduxikuer K, Wang JS. Four New Cases of SLC35A2-CDG With Novel Mutations and Clinical Features. Front Genet 2021; 12:658786. [PMID: 34122512 PMCID: PMC8191577 DOI: 10.3389/fgene.2021.658786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
SLC35A2-CDG is a rare type of X-linked CDG with more than 60 reported cases. We retrospectively analyzed clinical phenotypes and SLC35A2 genotypes of four cases of SLC35A2-CDG from four unrelated families of Han ethnicity in China. All patients had infantile onset epilepsies that were completely or partly resistant to multiple anti-epileptic medications or ketogenic diet. Three patients had severe developmental delay. All patients were female patients carrying de novo deleterious mutations in SLC35A2 (NM_001042498.2) gene, including one canonical splice-site mutation (c.426+1G > A), one large deletion (c.-322_c.274+1del), and two frameshift mutations leading to premature stop codon (c.781delC/p.Arg289ValfsTer88 and c.601delG/p.Ala201GlnfsTer148). Novel clinical features in some of our patients include anemia, hypertriglyceridemia, hypertonia, small ears, extra folds on earlobes, and maternal oligohydramnios or hypothyroidism during pregnancy. In one patient, concomitant Marfan syndrome was confirmed for having positive family history, carrying a heterozygous known disease-causing mutation in FBN1 gene (c.7240C > T/p.Arg2414Ter), and presence of typical features (rachnodactyly, ventrical septal defect, and mitral valve regurgitation). In conclusion, we expanded clinical phenotype and genetic mutation spectrum of SLC35A2-CDG by reporting four new cases with novel pathogenic variants and novel clinical features.
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Affiliation(s)
| | - Jian-She Wang
- Department of Hepatology, Children's Hospital of Fudan University, Shanghai, China
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16
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Dang LT, Vaid S, Lin G, Swaminathan P, Safran J, Loughman A, Lee M, Glenn T, Majolo F, Crino PB, Parent JM. STRADA-mutant human cortical organoids model megalencephaly and exhibit delayed neuronal differentiation. Dev Neurobiol 2021; 81:696-709. [PMID: 33619909 DOI: 10.1002/dneu.22816] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/31/2022]
Abstract
Genetic diseases involving overactivation of the mechanistic target of rapamycin (mTOR) pathway, so-called "mTORopathies," often manifest with malformations of cortical development (MCDs), epilepsy, and cognitive impairment. How mTOR pathway hyperactivation results in abnormal human cortical development is poorly understood. To study the effect of mTOR hyperactivity on early stages of cortical development, we focused on Pretzel Syndrome (polyhydramnios, megalencephaly, symptomatic epilepsy; PMSE syndrome), a rare mTORopathy caused by homozygous germline mutations in the STRADA gene. We developed a human cortical organoid (hCO) model of PMSE and examined morphology and size for the first 2 weeks of organoid growth, and cell type composition at weeks 2, 8, and 12 of differentiation. In the second week, PMSE hCOs enlarged more rapidly than controls and displayed an abnormal Wnt pathway-dependent increase in neural rosette structures. PMSE hCOs also exhibited delayed neurogenesis, decreased subventricular zone progenitors, increased proliferation and cell death, and an abnormal architecture of primary cilia. At week 8, PMSE hCOs had fewer deep layer neurons. By week 12, neurogenesis recovered in PMSE organoids, but they displayed increased outer radial glia, a cell type thought to contribute to the expansion of the human cerebral cortex. Together, these findings suggest that megalencephaly in PMSE arises from the expansion of neural stem cells in early corticogenesis and potentially also from increased outer radial glial at later gestational stages. The delayed neuronal differentiation in PMSE organoids demonstrates the important role the mTOR pathway plays in the maintenance and expansion of the stem cell pool.
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Affiliation(s)
- Louis T Dang
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA.,Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA.,Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, USA
| | - Shivanshi Vaid
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA.,Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, USA
| | - Grace Lin
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA.,Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, USA
| | | | - Jordan Safran
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Anna Loughman
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Monica Lee
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Trevor Glenn
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA
| | - Fernanda Majolo
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jack M Parent
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA.,Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, USA.,Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
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17
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Homozygous missense STRADA mutation in a patient with polyhydramnios, megalencephaly and symptomatic epilepsy syndrome. Clin Dysmorphol 2021; 30:121-124. [PMID: 33605605 DOI: 10.1097/mcd.0000000000000368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Homozygous or compound heterozygous mutations in STRADA cause polyhydramnios, megalencephaly and symptomatic epilepsy syndrome (PMSE), with additional features of distinctive facial traits and severe developmental delay or intellectual disability. This syndrome was first defined in 16 Old Order Mennonite patients, carrying a homozygous STRADA deletion of exon 9-13. Five additional PMSE patients have been reported since, each of them with loss-of-function variants. We report a female patient with the typical clinical features of PMSE, homozygous for a novel STRADA missense mutation c.792T>A (p.Ser264Arg) in exon 10. This finding contributes to the further delineation of the phenotype of PMSE.
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SLC35A2-CDG: Novel variant and review. Mol Genet Metab Rep 2021; 26:100717. [PMID: 33552911 PMCID: PMC7851840 DOI: 10.1016/j.ymgmr.2021.100717] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
SLC35A2 encodes the X-linked transporter that carries uridine diphosphate (UDP)-galactose from the cytosol to the lumen of the Golgi apparatus and the endoplasmic reticulum. Pathogenic variants have been associated to a congenital disorder of glycosylation (CDG) with epileptic encephalopathy as a predominant feature. Among the sixty five patients described so far, a strong gender bias is observed as only seven patients are males. This work is a review and reports a SLC35A2-CDG in a male without epilepsy and with growth deficiency associated with decreased serum IGF1, minor neurological involvement, minor facial dysmorphism, and camptodactyly of fingers and toes. Sequence analysis revealed a hemizygosity for a novel de novo variant: c.233A > G (p.Lys78Arg) in SLC35A2. Further analysis of SLC35A2 sequence by comparing both orthologous and paralogous positions, revealed that not only the variant found in this study, but also most of the reported mutated positions are conserved in SLC35A2 orthologous, and many even in the paralogous SLC35A1 and SLC35A3. This is strong evidence that replacements at these positions will have a critical pathological effect and may also explain the gender bias observed among SLC35A2-CDG patients.
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19
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20
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Dang LT, Glanowska KM, Iffland Ii PH, Barnes AE, Baybis M, Liu Y, Patino G, Vaid S, Streicher AM, Parker WE, Kim S, Moon UY, Henry FE, Murphy GG, Sutton M, Parent JM, Crino PB. Multimodal Analysis of STRADA Function in Brain Development. Front Cell Neurosci 2020; 14:122. [PMID: 32457579 PMCID: PMC7227375 DOI: 10.3389/fncel.2020.00122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
mTORopathies are a heterogeneous group of neurological disorders characterized by malformations of cortical development (MCD), enhanced cellular mechanistic target of rapamycin (mTOR) signaling, and epilepsy that results from mutations in mTOR pathway regulatory genes. Homozygous mutations (del exon 9–13) in the pseudokinase STE20-related kinase adaptor alpha (STRAD-α; STRADA), an mTOR modulator, are associated with Pretzel Syndrome (PS), a neurodevelopmental disorder within the Old Order Mennonite Community characterized by megalencephaly, intellectual disability, and intractable epilepsy. To study the cellular mechanisms of STRADA loss, we generated CRISPR-edited Strada mouse N2a cells, a germline mouse Strada knockout (KO−/−) strain, and induced pluripotent stem cell (iPSC)-derived neurons from PS individuals harboring the STRADA founder mutation. Strada KO in vitro leads to enhanced mTOR signaling and iPSC-derived neurons from PS individuals exhibit enhanced cell size and mTOR signaling activation, as well as subtle alterations in electrical firing properties e.g., increased input resistance, a more depolarized resting membrane potential, and decreased threshold for action potential (AP) generation. Strada−/− mice exhibit high rates of perinatal mortality and out of more than 100 litters yielding both WT and heterozygous pups, only eight Strada−/− animals survived past P5. Strada−/− mice are hypotonic and tremulous. Histopathological examination (n = 5 mice) revealed normal gross brain organization and lamination but all had ventriculomegaly. Ectopic neurons were seen in all five Strada−/− brains within the subcortical white matter mirroring what is observed in human PS brain tissue. These distinct experimental platforms demonstrate that STRADA modulates mTOR signaling and is a key regulator of cell size, neuronal excitability, and cortical lamination.
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Affiliation(s)
- Louis T Dang
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States.,Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Katarzyna M Glanowska
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States.,Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, United States
| | - Philip H Iffland Ii
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Allan E Barnes
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marianna Baybis
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yu Liu
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States
| | - Gustavo Patino
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States
| | - Shivanshi Vaid
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States.,Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | | | - Whitney E Parker
- Department of Neurosurgery, Weill-Cornell Medical Center, New York, NY, United States
| | - Seonhee Kim
- Louis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Uk Yeol Moon
- Louis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Frederick E Henry
- Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, United States.,Department of Molecular, and Integrative Physiology, Michigan Medicine, Ann Arbor, MI, United States
| | - Geoffrey G Murphy
- Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, United States.,Department of Molecular, and Integrative Physiology, Michigan Medicine, Ann Arbor, MI, United States
| | - Michael Sutton
- Michigan Neuroscience Institute, Michigan Medicine, Ann Arbor, MI, United States.,Department of Molecular, and Integrative Physiology, Michigan Medicine, Ann Arbor, MI, United States
| | - Jack M Parent
- Department of Neurology, Michigan Medicine, Ann Arbor, MI, United States.,Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, United States
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States
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21
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Malinowski J, Miller DT, Demmer L, Gannon J, Pereira EM, Schroeder MC, Scheuner MT, Tsai ACH, Hickey SE, Shen J. Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability. Genet Med 2020; 22:986-1004. [PMID: 32203227 PMCID: PMC7222126 DOI: 10.1038/s41436-020-0771-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose Exome and genome sequencing (ES/GS) are performed frequently in patients with congenital anomalies, developmental delay, or intellectual disability (CA/DD/ID), but the impact of results from ES/GS on clinical management and patient outcomes is not well characterized. A systematic evidence review (SER) can support future evidence-based guideline development for use of ES/GS in this patient population. Methods We undertook an SER to identify primary literature from January 2007 to March 2019 describing health, clinical, reproductive, and psychosocial outcomes resulting from ES/GS in patients with CA/DD/ID. A narrative synthesis of results was performed. Results We retrieved 2654 publications for full-text review from 7178 articles. Only 167 articles met our inclusion criteria, and these were primarily case reports or small case series of fewer than 20 patients. The most frequently reported outcomes from ES/GS were changes to clinical management or reproductive decision-making. Two studies reported on the reduction of mortality or morbidity or impact on quality of life following ES/GS. Conclusion There is evidence that ES/GS for patients with CA/DD/ID informs clinical and reproductive decision-making, which could lead to improved outcomes for patients and their family members. Further research is needed to generate evidence regarding health outcomes to inform robust guidelines regarding ES/GS in the care of patients with CA/DD/ID.
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Affiliation(s)
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Jennifer Gannon
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri, Kansas City, MO, USA
| | - Elaine Maria Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maren T Scheuner
- Division of Medical Genetics, Department of Pediatrics and Division of Hematology-Oncology, Department of Medicine, University of California, San Francisco, CA, USA.,San Francisco VA Healthcare System, San Francisco, CA, USA
| | - Anne Chun-Hui Tsai
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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22
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Lee Y, Park S, Lee JS, Kim SY, Cho J, Yoo Y, Lee S, Yoo T, Lee M, Seo J, Lee J, Kneissl J, Lee J, Jeon H, Jeon EY, Hong SE, Kim E, Kim H, Kim WJ, Kim JS, Ko JM, Cho A, Lim BC, Kim WS, Choi M, Chae JH. Genomic profiling of 553 uncharacterized neurodevelopment patients reveals a high proportion of recessive pathogenic variant carriers in an outbred population. Sci Rep 2020; 10:1413. [PMID: 31996704 PMCID: PMC6989631 DOI: 10.1038/s41598-020-58101-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/10/2020] [Indexed: 11/22/2022] Open
Abstract
A substantial portion of Mendelian disease patients suffers from genetic variants that are inherited in a recessive manner. A precise understanding of pathogenic recessive variants in a population would assist in pre-screening births of such patients. However, a systematic understanding of the contribution of recessive variants to Mendelian diseases is still lacking. Therefore, genetic diagnosis and variant discovery of 553 undiagnosed Korean patients with complex neurodevelopmental problems (KND for Korean NeuroDevelopmental cohort) were performed using whole exome sequencing of patients and their parents. Disease-causing variants, including newly discovered variants, were identified in 57.5% of the probands of the KND cohort. Among the patients with the previous reported pathogenic variants, 35.1% inherited these variants in a recessive manner. Genes that cause recessive disorders in our cohort tend to be less constrained by loss-of-function variants and were enriched in lipid metabolism and mitochondrial functions. This observation was applied to an estimation that approximately 1 in 17 healthy Korean individuals carry at least one of these pathogenic variants that develop severe neurodevelopmental problems in a recessive manner. Furthermore, the feasibility of these genes for carrier screening was evaluated. Our results will serve as a foundation for recessive variant screening to reduce occurrences of rare Mendelian disease patients. Additionally, our results highlight the utility and necessity of whole exome sequencing-based diagnostics for improving patient care in a country with a centralized medical system.
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Affiliation(s)
- Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Pediatrics, Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
- Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jaeso Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Moses Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jieun Seo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Interdisciplinary Program for Bioengineering, Graduate School, Seoul National Universty, Seoul, 03080, Republic of Korea
| | - Jana Kneissl
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eunha Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hyuna Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jon Soo Kim
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, 28644, Republic of Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Anna Cho
- Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, 07804, Republic of Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Won Seop Kim
- Department of Pediatrics, College of Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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23
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Lee CG, Jang JH, Seo JY. First identified Korean family with Tatton-Brown-Rahman Syndrome caused by the novel DNMT3A variant c.118G>C p.(Glu40Gln). Ann Pediatr Endocrinol Metab 2019; 24:253-256. [PMID: 31905446 PMCID: PMC6944862 DOI: 10.6065/apem.2019.24.4.253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 12/27/2022] Open
Abstract
Tatton-Brown-Rahman Syndrome (TBRS), an overgrowth syndrome caused by heterozygous mutation of DNMT3A, first was described in 2014. Approximately 60 DNMT3A variants, including 32 missense variants, have been reported, with most missense mutations located on the DNMT3A functional domains. Autosomal dominant inheritance by germ-line mutation of DNMT3A has been reported, but vertical transmission within a family is extremely rare. Herein, we report the first Korean family with maternally inherited TBRS due to the novel heterozygous DNMT3A variant c.118G>C p.(Glu40Gln), located outside the main functional domain and identified by multigene panel sequencing. The patient and her mother had typical clinical features, including tall stature during childhood, macrocephaly, intellectual disability, and characteristic facial appearance. TBRS shows milder dysmorphic features than other overgrowth syndromes, potentially leading to underdiagnosis and underestimated prevalence; thus, targeted multigene panel sequencing including DNMT3A will be a useful tool in cases of overgrowth and unexplained mild intellectual disability for early diagnosis and genetic counseling.
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Affiliation(s)
- Cha Gon Lee
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University, Seoul, Korea
| | | | - Ji-Young Seo
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University, Seoul, Korea
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24
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Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, Brunner H, Hoang N, Scherer SW, Sahin M, Miller DT. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med 2019; 21:2413-2421. [PMID: 31182824 PMCID: PMC6831729 DOI: 10.1038/s41436-019-0554-6] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose For neurodevelopmental disorders (NDDs), etiological evaluation can
be a diagnostic odyssey involving numerous genetic tests, underscoring the need
to develop a streamlined algorithm maximizing molecular diagnostic yield for
this clinical indication. Our objective was to compare the yield of exome
sequencing (ES) with that of chromosomal microarray (CMA), the current
first-tier test for NDDs. Methods We performed a PubMed scoping review and meta-analysis investigating
the diagnostic yield of ES for NDDs as the basis of a consensus development
conference. We defined NDD as global developmental delay, intellectual
disability, and/or autism spectrum disorder. The consensus development
conference included input from genetics professionals, pediatric neurologists,
and developmental behavioral pediatricians. Results After applying strict inclusion/exclusion criteria, we identified 30
articles with data on molecular diagnostic yield in individuals with isolated
NDD, or NDD plus associated conditions (such as Rett-like features). Yield of ES
was 36% overall, 31% for isolated NDD, and 53% for the NDD plus associated
conditions. ES yield for NDDs is markedly greater than previous studies of CMA
(15–20%). Conclusion Our review demonstrates that ES consistently outperforms CMA for
evaluation of unexplained NDDs. We propose a diagnostic algorithm placing ES at
the beginning of the evaluation of unexplained NDDs.
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Affiliation(s)
- Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie A Love-Nichols
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA.,SFARI, Simons Foundation, New York, NY, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Robin L Hansen
- MIND Institute, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lisa Prock
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Developmental Medicine Center, Boston Children's Hospital, Boston, MA, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.,The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
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25
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Demos M, Guella I, DeGuzman C, McKenzie MB, Buerki SE, Evans DM, Toyota EB, Boelman C, Huh LL, Datta A, Michoulas A, Selby K, Bjornson BH, Horvath G, Lopez-Rangel E, van Karnebeek CDM, Salvarinova R, Slade E, Eydoux P, Adam S, Van Allen MI, Nelson TN, Bolbocean C, Connolly MB, Farrer MJ. Diagnostic Yield and Treatment Impact of Targeted Exome Sequencing in Early-Onset Epilepsy. Front Neurol 2019; 10:434. [PMID: 31164858 PMCID: PMC6536592 DOI: 10.3389/fneur.2019.00434] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
Targeted whole-exome sequencing (WES) is a powerful diagnostic tool for a broad spectrum of heterogeneous neurological disorders. Here, we aim to examine the impact on diagnosis, treatment and cost with early use of targeted WES in early-onset epilepsy. WES was performed on 180 patients with early-onset epilepsy (≤5 years) of unknown cause. Patients were classified as Retrospective (epilepsy diagnosis >6 months) or Prospective (epilepsy diagnosis <6 months). WES was performed on an Ion Proton™ and variant reporting was restricted to the sequences of 620 known epilepsy genes. Diagnostic yield and time to diagnosis were calculated. An analysis of cost and impact on treatment was also performed. A molecular diagnoses (pathogenic/likely pathogenic variants) was achieved in 59/180 patients (33%). Clinical management changed following WES findings in 23 of 59 diagnosed patients (39%) or 13% of all patients. A possible diagnosis was identified in 21 additional patients (12%) for whom supporting evidence is pending. Time from epilepsy onset to a genetic diagnosis was faster when WES was performed early in the diagnostic process (mean: 145 days Prospective vs. 2,882 days Retrospective). Costs of prior negative tests averaged $8,344 per patient in the Retrospective group, suggesting savings of $5,110 per patient using WES. These results highlight the diagnostic yield, clinical utility and potential cost-effectiveness of using targeted WES early in the diagnostic workup of patients with unexplained early-onset epilepsy. The costs and clinical benefits are likely to continue to improve. Advances in precision medicine and further studies regarding impact on long-term clinical outcome will be important.
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Affiliation(s)
- Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Ilaria Guella
- Department of Medical Genetics, Centre for Applied Neurogenetics (CAN), University of British Columbia, Vancouver, BC, Canada
| | - Conrado DeGuzman
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Marna B McKenzie
- Department of Medical Genetics, Centre for Applied Neurogenetics (CAN), University of British Columbia, Vancouver, BC, Canada
| | - Sarah E Buerki
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada.,Division of Neuropediatrics, University Children's Hospital Zurich, Zurich, Switzerland
| | - Daniel M Evans
- Department of Medical Genetics, Centre for Applied Neurogenetics (CAN), University of British Columbia, Vancouver, BC, Canada
| | - Eric B Toyota
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Cyrus Boelman
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Linda L Huh
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Anita Datta
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Aspasia Michoulas
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Bruce H Bjornson
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Gabriella Horvath
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Elena Lopez-Rangel
- Division of Developmental Pediatrics, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Clara D M van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, BCCHRI, University of British Columbia, Vancouver, BC, Canada.,Department of Pediatrics, Academic Medical Centre, Amsterdam, Netherlands
| | - Ramona Salvarinova
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Erin Slade
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Patrice Eydoux
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Shelin Adam
- Department of Medical Genetics, BC Children's and BC's Women's Hospitals, University of British Columbia, Vancouver, BC, Canada
| | - Margot I Van Allen
- Department of Medical Genetics, BC Children's and BC's Women's Hospitals, University of British Columbia, Vancouver, BC, Canada
| | - Tanya N Nelson
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Corneliu Bolbocean
- University of Tennessee Health Science Center, Memphis, TN, United States.,Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Mary B Connolly
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Matthew J Farrer
- Department of Medical Genetics, Centre for Applied Neurogenetics (CAN), University of British Columbia, Vancouver, BC, Canada
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26
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Vals MA, Ashikov A, Ilves P, Loorits D, Zeng Q, Barone R, Huijben K, Sykut-Cegielska J, Diogo L, Elias AF, Greenwood RS, Grunewald S, van Hasselt PM, van de Kamp JM, Mancini G, Okninska A, Pajusalu S, Rudd PM, Rustad CF, Salvarinova R, de Vries BBA, Wolf NI, Ng BG, Freeze HH, Lefeber DJ, Õunap K. Clinical, neuroradiological, and biochemical features of SLC35A2-CDG patients. J Inherit Metab Dis 2019; 42:553-564. [PMID: 30746764 DOI: 10.1002/jimd.12055] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 11/10/2022]
Abstract
SLC35A2-CDG is caused by mutations in the X-linked SLC35A2 gene encoding the UDP-galactose transporter. SLC35A2 mutations lead to hypogalactosylation of N-glycans. SLC35A2-CDG is characterized by severe neurological symptoms and, in many patients, early-onset epileptic encephalopathy. In view of the diagnostic challenges, we studied the clinical, neuroradiological, and biochemical features of 15 patients (11 females and 4 males) with SLC35A2-CDG from various centers. We describe nine novel pathogenic variations in SLC35A2. All affected individuals presented with a global developmental delay, and hypotonia, while 70% were nonambulatory. Epilepsy was present in 80% of the patients, and in EEG hypsarrhythmia and findings consistent with epileptic encephalopathy were frequently seen. The most common brain MRI abnormality was cerebral atrophy with delayed myelination and multifocal inhomogeneous abnormal patchy white matter hyperintensities, which seemed to be nonprogressive. Thin corpus callosum was also common, and all the patients had a corpus callosum shorter than normal for their age. Variable dysmorphic features and growth deficiency were noted. Biochemically, normal mucin type O-glycosylation and lipid glycosylation were found, while transferrin mass spectrometry was found to be more specific in the identification of SLC35A2-CDG, as compared to routine screening tests. Although normal glycosylation studies together with clinical variability and genetic results complicate the diagnosis of SLC35A2-CDG, our data indicate that the combination of these three elements can support the pathogenicity of mutations in SLC35A2.
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Affiliation(s)
- Mari-Anne Vals
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Children's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Angel Ashikov
- Donders Institute for Brain, Cognition, and Behavior, Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pilvi Ilves
- Radiology Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Radiology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Dagmar Loorits
- Radiology Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Radiology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Qiang Zeng
- GlycoScience Group, National Institute for Bioprocessing Research & Training, Dublin, Ireland
| | - Rita Barone
- Child Neurology and Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- Department of Clinical and Experimental Medicine, Referral Centre for Inherited Metabolic Diseases, University of Catania, Catania, Italy
| | - Karin Huijben
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Paediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Luísa Diogo
- Child Developmental Center, Hospital Pediátrico, Center for Inherited Metabolic Diseases, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, Montana
| | - Robert S Greenwood
- Department of Neurology, University of North Carolina School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephanie Grunewald
- Metabolic Unit, Great Ormond Street Hospital and Institute of Child Health, University College London, NHS Trust, London, UK
| | - Peter M van Hasselt
- Division Pediatrics, Metabolic Diseases, Wilhelmina Children's Hospital (Part of UMC Utrecht), Utrecht, The Netherlands
| | - Jiddeke M van de Kamp
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Grazia Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Agnieszka Okninska
- Clinic of Children and Adolescent Neurology, Institute of Mother and Child, Warsaw, Poland
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pauline M Rudd
- GlycoScience Group, National Institute for Bioprocessing Research & Training, Dublin, Ireland
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ramona Salvarinova
- Division of Biochemical Diseases, Department of Pediatrics, British Columbia Children's Hospital, UBC BC Children's Hospital Research Institute, Vancouver, Canada
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicole I Wolf
- Department of Child Neurology and Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Dirk J Lefeber
- Donders Institute for Brain, Cognition, and Behavior, Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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27
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Dikow N, Moog U, Karch S, Sander A, Kilian S, Blank R, Reuner G. What do parents expect from a genetic diagnosis of their child with intellectual disability? JOURNAL OF APPLIED RESEARCH IN INTELLECTUAL DISABILITIES 2019; 32:1129-1137. [PMID: 30983121 DOI: 10.1111/jar.12602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 02/28/2019] [Accepted: 03/22/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Caring for a child with intellectual disability (ID) has been associated with increased social and psychological burdens. Diagnostic and prognostic uncertainty may enhance emotional stress in families. METHOD The present authors assessed the motivations, expectations, mental health, physical health and the quality of life of 194 parents whose children with intellectual disability were undergoing a genetic diagnostic workup. RESULTS Most parents considered a diagnosis highly relevant for their own emotional relief, their child's therapies and education, or family planning. Parental mental health was significantly lower compared with the normative sample, but physical health was not different. The severity of the child's intellectual disability correlated negatively with their parents' mental and physical health, quality of life, and positively with parental anxiety. CONCLUSION Healthcare providers should be aware of the disadvantages facing families with intellectually disabled children. Receiving practical, social and psychological support as well as genetic testing might be particularly relevant for families with severely disabled children.
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Affiliation(s)
- Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Stephanie Karch
- Section for Neuropediatrics and Inborn Errors of Metabolism, University Children's Hospital, Clinic I, Heidelberg, Germany
| | - Anja Sander
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Samuel Kilian
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Rainer Blank
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Gitta Reuner
- Section for Neuropediatrics and Inborn Errors of Metabolism, University Children's Hospital, Clinic I, Heidelberg, Germany
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28
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Mühlebner A, Bongaarts A, Sarnat HB, Scholl T, Aronica E. New insights into a spectrum of developmental malformations related to mTOR dysregulations: challenges and perspectives. J Anat 2019; 235:521-542. [PMID: 30901081 DOI: 10.1111/joa.12956] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years the role of the mammalian target of rapamycin (mTOR) pathway has emerged as crucial for normal cortical development. Therefore, it is not surprising that aberrant activation of mTOR is associated with developmental malformations and epileptogenesis. A broad spectrum of malformations of cortical development, such as focal cortical dysplasia (FCD) and tuberous sclerosis complex (TSC), have been linked to either germline or somatic mutations in mTOR pathway-related genes, commonly summarised under the umbrella term 'mTORopathies'. However, there are still a number of unanswered questions regarding the involvement of mTOR in the pathophysiology of these abnormalities. Therefore, a monogenetic disease, such as TSC, can be more easily applied as a model to study the mechanisms of epileptogenesis and identify potential new targets of therapy. Developmental neuropathology and genetics demonstrate that FCD IIb and hemimegalencephaly are the same diseases. Constitutive activation of mTOR signalling represents a shared pathogenic mechanism in a group of developmental malformations that have histopathological and clinical features in common, such as epilepsy, autism and other comorbidities. We seek to understand the effect of mTOR dysregulation in a developing cortex with the propensity to generate seizures as well as the aftermath of the surrounding environment, including the white matter.
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Affiliation(s)
- A Mühlebner
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A Bongaarts
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - H B Sarnat
- Departments of Paediatrics, Pathology (Neuropathology) and Clinical Neurosciences, University of Calgary Cumming School of Medicine and Alberta Children's Hospital Research Institute (Owerko Centre), Calgary, AB, Canada
| | - T Scholl
- Department of Paediatric and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - E Aronica
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Amsterdam, The Netherlands
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29
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Ott T, Kaufmann L, Granzow M, Hinderhofer K, Bartram CR, Theiß S, Seitz A, Paramasivam N, Schulz A, Moog U, Blum M, Evers CM. The Frog Xenopus as a Model to Study Joubert Syndrome: The Case of a Human Patient With Compound Heterozygous Variants in PIBF1. Front Physiol 2019; 10:134. [PMID: 30858804 PMCID: PMC6397843 DOI: 10.3389/fphys.2019.00134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Joubert syndrome (JS) is a congenital autosomal-recessive or—in rare cases–X-linked inherited disease. The diagnostic hallmark of the so-called molar tooth sign describes the morphological manifestation of the mid- and hind-brain in axial brain scans. Affected individuals show delayed development, intellectual disability, ataxia, hyperpnea, sleep apnea, abnormal eye, and tongue movements as well as hypotonia. At the cellular level, JS is associated with the compromised biogenesis of sensory cilia, which identifies JS as a member of the large group of ciliopathies. Here we report on the identification of novel compound heterozygous variants (p.Y503C and p.Q485*) in the centrosomal gene PIBF1 in a patient with JS via trio whole exome sequencing. We have studied the underlying disease mechanism in the frog Xenopus, which offers fast assessment of cilia functions in a number of embryological contexts. Morpholino oligomer (MO) mediated knockdown of the orthologous Xenopus pibf1 gene resulted in defective mucociliary clearance in the larval epidermis, due to reduced cilia numbers and motility on multiciliated cells. To functionally assess patient alleles, mutations were analyzed in the larval skin: the p.Q485* nonsense mutation resulted in a disturbed localization of PIBF1 to the ciliary base. This mutant failed to rescue the ciliation phenotype following knockdown of endogenous pibf1. In contrast, the missense variant p.Y503C resulted in attenuated rescue capacity compared to the wild type allele. Based on these results, we conclude that in the case of this patient, JS is the result of a pathogenic combination of an amorphic and a hypomorphic PIBF1 allele. Our study underscores the versatility of the Xenopus model to study ciliopathies such as JS in a rapid and cost-effective manner, which should render this animal model attractive for future studies of human ciliopathies.
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Affiliation(s)
- Tim Ott
- Institute of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Claus R Bartram
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Susanne Theiß
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika Seitz
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.,Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Schulz
- Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Martin Blum
- Institute of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Christina M Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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30
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Khan TN, Khan K, Sadeghpour A, Reynolds H, Perilla Y, McDonald MT, Gallentine WB, Baig SM, Davis EE, Katsanis N. Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies. Am J Hum Genet 2019; 104:94-111. [PMID: 30609410 PMCID: PMC6323578 DOI: 10.1016/j.ajhg.2018.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
The use of whole-exome and whole-genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here, we report on two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects, failure to thrive, ocular abnormalities, and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous NPHP1 deletion, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules in zebrafish larvae. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy, and they highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus.
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Affiliation(s)
- Tahir N Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hannah Reynolds
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Furman University, Greenville, SC 29613, USA
| | - Yezmin Perilla
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - William B Gallentine
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
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31
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Alkhater RA, Scherer SW, Minassian BA, Walker S. PI4K2A deficiency in an intellectual disability, epilepsy, myoclonus, akathisia syndrome. Ann Clin Transl Neurol 2018; 5:1617-1621. [PMID: 30564627 PMCID: PMC6292187 DOI: 10.1002/acn3.677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023] Open
Abstract
We report a family of Saudi Arabian ancestry with two children presenting with global developmental delay, dystonia, disturbed sleep, and heat intolerance. By genome sequencing, we identified a nonsense variant in the first exon of PI4K2A that was homozygous in both affected individuals and was absent from, or heterozygous in, seven unaffected siblings. PI4K2A is highly expressed in the brain and a mouse model displays a neurological phenotype, implicating PI4K2A as a new disease gene for a neurological disorder.
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Affiliation(s)
- Reem A Alkhater
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto Ontario Canada.,Johns' Hopkins Aramco Healthcare Dhahran Saudi Arabia
| | - Stephen W Scherer
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto Ontario Canada.,The Centre for Applied Genomics The Hospital for Sick Children Toronto Ontario Canada.,Department of Molecular Genetics University of Toronto Toronto Canada.,McLaughlin Centre University of Toronto Toronto Canada
| | - Berge A Minassian
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto Ontario Canada.,Department of Pediatrics University of Texas Southwestern Dallas Texas
| | - Susan Walker
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto Ontario Canada.,The Centre for Applied Genomics The Hospital for Sick Children Toronto Ontario Canada
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32
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Yates TM, Suri M, Desurkar A, Lesca G, Wallgren-Pettersson C, Hammer TB, Raghavan A, Poulat AL, Møller RS, Thuresson AC, Balasubramanian M. SLC35A2-related congenital disorder of glycosylation: Defining the phenotype. Eur J Paediatr Neurol 2018; 22:1095-1102. [PMID: 30194038 DOI: 10.1016/j.ejpn.2018.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/10/2018] [Accepted: 08/19/2018] [Indexed: 12/01/2022]
Abstract
We aim to further delineate the phenotype associated with pathogenic variants in the SLC35A2 gene, and review all published literature to-date. This gene is located on the X chromosome and encodes a UDP-galactose transporter. Pathogenic variants in SLC35A2 cause a congenital disorder of glycosylation. The condition is rare, and less than twenty patients have been reported to-date. The phenotype is complex and has not been fully defined. Here, we present a series of five patients with de novo pathogenic variants in SLC35A2. The patients' phenotype includes developmental and epileptic encephalopathy with hypsarrhythmia, facial dysmorphism, severe intellectual disability, skeletal abnormalities, congenital cardiac disease and cortical visual impairment. Developmental and epileptic encephalopathy with hypsarrhythmia is present in most patients with SLC35A2 variants, and is drug-resistant in the majority of cases. Adrenocorticotropic hormone therapy may achieve partial or complete remission of seizures, but the effect is usually temporary. Isoelectric focusing of transferrins may be normal after infancy, therefore a congenital disorder of glycosylation should still be considered as a diagnosis in the presence of a suggestive phenotype. We also provide evidence that cortical visual impairment is part of the phenotypic spectrum.
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Affiliation(s)
- T Michael Yates
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, UK
| | - Archana Desurkar
- Department of Paediatric Neurology, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Gaetan Lesca
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France
| | - Carina Wallgren-Pettersson
- Department of Medical and Clinical Genetics, University of Helsinki and the Folkhaelsan Institute of Genetics, Helsinki, Finland
| | - Trine B Hammer
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark
| | - Ashok Raghavan
- Department of Radiology, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Anne-Lise Poulat
- Hospices Civils de Lyon, Service de Génétique, CHU de Lyon, Lyon, France
| | - Rikke S Møller
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark; Institute for Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK; Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, UK.
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33
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van Karnebeek CDM, Wortmann SB, Tarailo-Graovac M, Langeveld M, Ferreira CR, van de Kamp JM, Hollak CE, Wasserman WW, Waterham HR, Wevers RA, Haack TB, Wanders RJA, Boycott KM. The role of the clinician in the multi-omics era: are you ready? J Inherit Metab Dis 2018; 41:571-582. [PMID: 29362952 PMCID: PMC5959952 DOI: 10.1007/s10545-017-0128-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022]
Abstract
Since Garrod's first description of alkaptonuria in 1902, and newborn screening for phenylketonuria introduced in the 1960s, P4 medicine (preventive, predictive, personalized, and participatory) has been a reality for the clinician serving patients with inherited metabolic diseases. The era of high-throughput technologies promises to accelerate its scale dramatically. Genomics, transcriptomics, epigenomics, proteomics, glycomics, metabolomics, and lipidomics offer an amazing opportunity for holistic investigation and contextual pathophysiologic understanding of inherited metabolic diseases for precise diagnosis and tailored treatment. While each of the -omics technologies is important to systems biology, some are more mature than others. Exome sequencing is emerging as a reimbursed test in clinics around the world, and untargeted metabolomics has the potential to serve as a single biochemical testing platform. The challenge lies in the integration and cautious interpretation of these big data, with translation into clinically meaningful information and/or action for our patients. A daunting but exciting task for the clinician; we provide clinical cases to illustrate the importance of his/her role as the connector between physicians, laboratory experts and researchers in the basic, computer, and clinical sciences. Open collaborations, data sharing, functional assays, and model organisms play a key role in the validation of -omics discoveries. Having all the right expertise at the table when discussing the diagnostic approach and individualized management plan according to the information yielded by -omics investigations (e.g., actionable mutations, novel therapeutic interventions), is the stepping stone of P4 medicine. Patient participation and the adjustment of the medical team's plan to his/her and the family's wishes most certainly is the capstone. Are you ready?
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Affiliation(s)
- Clara D M van Karnebeek
- Department of Pediatrics and Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands.
- Departments of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, BC, Canada.
- Deparment of Pediatrics (Room H7-224), Emma Children's Hospital, Academic Medical Centre, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Maja Tarailo-Graovac
- Departments of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, BC, Canada
- Departments of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, Vancouver, BC, Canada
- Departments of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, CA, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, CA, Canada
| | - Mirjam Langeveld
- Department of Endocrinology and Metabolism, Academic Medical Centre, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiddeke M van de Kamp
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Carla E Hollak
- Department of Endocrinology and Metabolism, Academic Medical Centre, Amsterdam, The Netherlands
| | - Wyeth W Wasserman
- Departments of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, BC, Canada
- Departments of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, Vancouver, BC, Canada
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Laboratory Division & Department of Pediatrics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Laboratory Division & Department of Pediatrics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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34
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Mattick JS, Dinger M, Schonrock N, Cowley M. Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing. Med J Aust 2018; 209:197-199. [DOI: 10.5694/mja17.01176] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- John S Mattick
- Garvan Institute of Medical Research, Sydney, NSW
- St Vincentˈs Clinical School, UNSW Sydney, Sydney, NSW
| | - Marcel Dinger
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Nicole Schonrock
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Mark Cowley
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
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Dimitrov B, Himmelreich N, Hipgrave Ederveen AL, Lüchtenborg C, Okun JG, Breuer M, Hutter AM, Carl M, Guglielmi L, Hellwig A, Thiemann KC, Jost M, Peters V, Staufner C, Hoffmann GF, Hackenberg A, Paramasivam N, Wiemann S, Eils R, Schlesner M, Strahl S, Brügger B, Wuhrer M, Christoph Korenke G, Thiel C. Cutis laxa, exocrine pancreatic insufficiency and altered cellular metabolomics as additional symptoms in a new patient with ATP6AP1-CDG. Mol Genet Metab 2018; 123:364-374. [PMID: 29396028 DOI: 10.1016/j.ymgme.2018.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 02/07/2023]
Abstract
Congenital disorders of glycosylation (CDG) are genetic defects in the glycoconjugate biosynthesis. >100 types of CDG are known, most of them cause multi-organ diseases. Here we describe a boy whose leading symptoms comprise cutis laxa, pancreatic insufficiency and hepatosplenomegaly. Whole exome sequencing identified the novel hemizygous mutation c.542T>G (p.L181R) in the X-linked ATP6AP1, an accessory protein of the mammalian vacuolar H+-ATPase, which led to a general N-glycosylation deficiency. Studies of serum N-glycans revealed reduction of complex sialylated and appearance of truncated diantennary structures. Proliferation of the patient's fibroblasts was significantly reduced and doubling time prolonged. Additionally, there were alterations in the fibroblasts' amino acid levels and the acylcarnitine composition. Especially, short-chain species were reduced, whereas several medium- to long-chain acylcarnitines (C14-OH to C18) were elevated. Investigation of the main lipid classes revealed that total cholesterol was significantly enriched in the patient's fibroblasts at the expense of phophatidylcholine and phosphatidylethanolamine. Within the minor lipid species, hexosylceramide was reduced, while its immediate precursor ceramide was increased. Since catalase activity and ACOX3 expression in peroxisomes were reduced, we assume an ATP6AP1-dependent impact on the β-oxidation of fatty acids. These results help to understand the complex clinical characteristics of this new patient.
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Affiliation(s)
- Bianca Dimitrov
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Nastassja Himmelreich
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Agnes L Hipgrave Ederveen
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jürgen G Okun
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Maximilian Breuer
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Anna-Marlen Hutter
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Matthias Carl
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Laboratory of Translational Neurogenetics, Center for Integrative Biology, University of Trento, 39123 Trento, Italy
| | - Luca Guglielmi
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Laboratory of Translational Neurogenetics, Center for Integrative Biology, University of Trento, 39123 Trento, Italy
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Kai Christian Thiemann
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Markus Jost
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Verena Peters
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Christian Staufner
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Georg F Hoffmann
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Annette Hackenberg
- Division of Pediatric Neurology, University Children's Hospital Zürich, Steinwiesstrasse 75, 8032 Zürich, Switzerland
| | - Nagarajan Paramasivam
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB), BioQuant, Heidelberg University, 69120 Heidelberg, Germany; Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - G Christoph Korenke
- Klinikum Oldenburg, Zentrum für Kinder-und Jugendmedizin, Klinik für Neuropädiatrie u. angeborene Stoffwechselerkrankungen, Rahel-Straus-Straße 10, 26133 Oldenburg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department I, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany.
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Curatolo P, Moavero R, van Scheppingen J, Aronica E. mTOR dysregulation and tuberous sclerosis-related epilepsy. Expert Rev Neurother 2018; 18:185-201. [DOI: 10.1080/14737175.2018.1428562] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University Hospital, Rome, Italy
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University Hospital, Rome, Italy
- Child Neurology Unit, Neuroscience and Neurorehabilitation Department, “Bambino Gesù” Children’s Hospital, IRCCS, Rome, Italy
| | - Jackelien van Scheppingen
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), The Netherlands
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Urreizti R, Damanti S, Esteve C, Franco-Valls H, Castilla-Vallmanya L, Tonda R, Cormand B, Vilageliu L, Opitz JM, Neri G, Grinberg D, Balcells S. A De Novo FOXP1 Truncating Mutation in a Patient Originally Diagnosed as C Syndrome. Sci Rep 2018; 8:694. [PMID: 29330474 PMCID: PMC5766530 DOI: 10.1038/s41598-017-19109-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/21/2017] [Indexed: 01/04/2023] Open
Abstract
De novo FOXP1 mutations have been associated with intellectual disability (ID), motor delay, autistic features and a wide spectrum of speech difficulties. C syndrome (Opitz C trigonocephaly syndrome) is a rare and genetically heterogeneous condition, characterized by trigonocephaly, craniofacial anomalies and ID. Several different chromosome deletions and and point mutations in distinct genes have been associated with the disease in patients originally diagnosed as Opitz C. By whole exome sequencing we identified a de novo splicing mutation in FOXP1 in a patient, initially diagnosed as C syndrome, who suffers from syndromic intellectual disability with trigonocephaly. The mutation (c.1428 + 1 G > A) promotes the skipping of exon 16, a frameshift and a premature STOP codon (p.Ala450GLyfs*13), as assessed by a minigene strategy. The patient reported here shares speech difficulties, intellectual disability and autistic features with other FOXP1 syndrome patients, and thus the diagnosis for this patient should be changed. Finally, since trigonocephaly has not been previously reported in FOXP1 syndrome, it remains to be proved whether it may be associated with the FOXP1 mutation.
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Affiliation(s)
- Roser Urreizti
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain.
| | - Sarah Damanti
- Geriatric Unit, Fondazione Ca'Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy.,Nutritional Sciences, University of Milan, Milan, Italy
| | - Carla Esteve
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Héctor Franco-Valls
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bru Cormand
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Lluïsa Vilageliu
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - John M Opitz
- Pediatrics Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Giovanni Neri
- Istituto di Medicina Genomica, Università Cattolica Sacro Cuore, Policlinico A. Gemelli, Rome, Italy
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Susana Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
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Dragojlovic N, Elliott AM, Adam S, van Karnebeek C, Lehman A, Mwenifumbo JC, Nelson TN, du Souich C, Friedman JM, Lynd LD. The cost and diagnostic yield of exome sequencing for children with suspected genetic disorders: a benchmarking study. Genet Med 2018; 20:1013-1021. [PMID: 29300375 DOI: 10.1038/gim.2017.226] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE This study aimed to generate benchmark estimates for the cost, diagnostic yield, and cost per positive diagnosis of diagnostic exome sequencing (ES) in heterogeneous pediatric patient populations and to illustrate how the design of an ES service can influence its cost and yield. METHODS A literature review and Monte Carlo simulations were used to generate benchmark estimates for singleton and trio ES. A cost model for the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, which is testing a proposed delivery model for diagnostic ES in British Columbia, is used to illustrate the potential effects of changing the service design. RESULTS The benchmark diagnostic yield was 34.3% (95% confidence interval (CI): 23.2-46.5) for trio ES and 26.5% (95% CI: 12.9-42.9) for singleton ES. The benchmark cost of delivery was C$6,437 (95% CI: $5,305-$7,704) in 2016 Canadian dollars (US$4,859; 4,391€) for trio ES and C$2,576 (95% CI: $1,993-$3,270) (US$1,944; 1,757€) for singleton ES. Scenario models for CAUSES suggest that alternative service designs could reduce costs but might lead to a higher cost per diagnosis due to lower yields. CONCLUSION Broad conclusions about the cost-effectiveness of ES should be drawn with caution when relying on studies that use cost or yield assumptions that lie at the extremes of the benchmark ranges.
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Affiliation(s)
- Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Shelin Adam
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.,Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Anna Lehman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jill C Mwenifumbo
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tanya N Nelson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, British Columbia, Canada.
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De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. Am J Hum Genet 2017; 101:768-788. [PMID: 29100089 DOI: 10.1016/j.ajhg.2017.10.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/09/2017] [Indexed: 02/08/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway.
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