1
|
Niceta M, Ciolfi A, Ferilli M, Pedace L, Cappelletti C, Nardini C, Hildonen M, Chiriatti L, Miele E, Dentici ML, Gnazzo M, Cesario C, Pisaneschi E, Baban A, Novelli A, Maitz S, Selicorni A, Squeo GM, Merla G, Dallapiccola B, Tumer Z, Digilio MC, Priolo M, Tartaglia M. DNA methylation profiling in Kabuki syndrome: reclassification of germline KMT2D VUS and sensitivity in validating postzygotic mosaicism. Eur J Hum Genet 2024; 32:819-826. [PMID: 38528056 PMCID: PMC11220151 DOI: 10.1038/s41431-024-01597-9] [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: 11/23/2023] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
Autosomal dominant Kabuki syndrome (KS) is a rare multiple congenital anomalies/neurodevelopmental disorder caused by heterozygous inactivating variants or structural rearrangements of the lysine-specific methyltransferase 2D (KMT2D) gene. While it is often recognizable due to a distinctive gestalt, the disorder is clinically variable, and a phenotypic scoring system has been introduced to help clinicians to reach a clinical diagnosis. The phenotype, however, can be less pronounced in some patients, including those carrying postzygotic mutations. The full spectrum of pathogenic variation in KMT2D has not fully been characterized, which may hamper the clinical classification of a portion of these variants. DNA methylation (DNAm) profiling has successfully been used as a tool to classify variants in genes associated with several neurodevelopmental disorders, including KS. In this work, we applied a KS-specific DNAm signature in a cohort of 13 individuals with KMT2D VUS and clinical features suggestive or overlapping with KS. We succeeded in correctly classifying all the tested individuals, confirming diagnosis for three subjects and rejecting the pathogenic role of 10 VUS in the context of KS. In the latter group, exome sequencing allowed to identify the genetic cause underlying the disorder in three subjects. By testing five individuals with postzygotic pathogenic KMT2D variants, we also provide evidence that DNAm profiling has power to recognize pathogenic variants at different levels of mosaicism, identifying 15% as the minimum threshold for which DNAm profiling can be applied as an informative diagnostic tool in KS mosaics.
Collapse
Affiliation(s)
- Marcello Niceta
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Marco Ferilli
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
- Department of Computer, Control and Management Engineering, Sapienza University, 00185, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Claudia Nardini
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Mathis Hildonen
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshopsitalet, 2600, Glostrup, Denmark
| | - Luigi Chiriatti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Elisa Pisaneschi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Anwar Baban
- Pediatric Cardiology and Cardiac Arrhythmias Unit, Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Silvia Maitz
- Genetica Clinica Pediatrica, Fondazione MBBM, ASST Monza Ospedale San Gerardo, 20900, Monza, Italy
| | | | - Gabriella Maria Squeo
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Zeynep Tumer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshopsitalet, 2600, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | | | - Manuela Priolo
- Medical and Laboratory Genetics, Antonio Cardarelli Hospital, 80131, Naples, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
| |
Collapse
|
2
|
Jansen NA, Cestèle S, Marco SS, Schenke M, Stewart K, Patel J, Tolner EA, Brunklaus A, Mantegazza M, van den Maagdenberg AMJM. Brainstem depolarization-induced lethal apnea associated with gain-of-function SCN1AL263V is prevented by sodium channel blockade. Proc Natl Acad Sci U S A 2024; 121:e2309000121. [PMID: 38547067 PMCID: PMC10998578 DOI: 10.1073/pnas.2309000121] [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: 06/05/2023] [Accepted: 02/21/2024] [Indexed: 04/02/2024] Open
Abstract
Apneic events are frightening but largely benign events that often occur in infants. Here, we report apparent life-threatening apneic events in an infant with the homozygous SCN1AL263V missense mutation, which causes familial hemiplegic migraine type 3 in heterozygous family members, in the absence of epilepsy. Observations consistent with the events in the infant were made in an Scn1aL263V knock-in mouse model, in which apnea was preceded by a large brainstem DC-shift, indicative of profound brainstem depolarization. The L263V mutation caused gain of NaV1.1 function effects in transfected HEK293 cells. Sodium channel blockade mitigated the gain-of-function characteristics, rescued lethal apnea in Scn1aL263V mice, and decreased the frequency of severe apneic events in the patient. Hence, this study shows that SCN1AL263V can cause life-threatening apneic events, which in a mouse model were caused by profound brainstem depolarization. In addition to being potentially relevant to sudden infant death syndrome pathophysiology, these data indicate that sodium channel blockers may be considered therapeutic for apneic events in patients with these and other gain-of-function SCN1A mutations.
Collapse
Affiliation(s)
- Nico A. Jansen
- Department of Human Genetics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Sandrine Cestèle
- Université Côte d’Azur, Valbonne-Sophia Antipolis06560, France
- Institute of Molecular and Cellular Pharmacology, Valbonne-Sophia Antipolis06560, France
| | - Silvia Sanchez Marco
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, University Hospitals Bristol, BristolBS2 8BJ, United Kingdom
| | - Maarten Schenke
- Department of Human Genetics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Kirsty Stewart
- West of Scotland Genetic Services, Queen Elizabeth University Hospital, GlasgowG51 4TF, United Kingdom
| | - Jayesh Patel
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, University Hospitals Bristol, BristolBS2 8BJ, United Kingdom
| | - Else A. Tolner
- Department of Human Genetics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden2333 ZA, The Netherlands
| | - Andreas Brunklaus
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, GlasgowG51 4TF, United Kingdom
- School of Health and Wellbeing, University of Glasgow, GlasgowG12 8TB, United Kingdom
| | - Massimo Mantegazza
- Université Côte d’Azur, Valbonne-Sophia Antipolis06560, France
- Institute of Molecular and Cellular Pharmacology, Valbonne-Sophia Antipolis06560, France
- Inserm, Valbonne-Sophia Antipolis06560, France
| | - Arn M. J. M. van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden2333 ZA, The Netherlands
| |
Collapse
|
3
|
Goldstein RD, Poduri A. Seizures and Sudden Death Beyond SUDEP. Neurology 2024; 102:e208119. [PMID: 38175993 DOI: 10.1212/wnl.0000000000208119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024] Open
Abstract
Many physicians and researchers are familiar with the tragic phenomenon known as sudden infant death syndrome (SIDS), the leading cause of postneonatal mortality in high-resource countries. A less familiar category of unexplained deaths is the problem of sudden unexplained death in childhood (SUDC), a more rare and unusual presentation of sudden death in children who are no longer infants and whose reasons for death defy explanation. A substantial body of research in SUDC now supports the possibility of an overlap with epilepsy and associated sudden death in that context (SUDEP). Stemming from the first contemporary reports of SUDC, we have learned that a disproportionate number of these children have personal and/or family histories of febrile seizures,1 in many cases, inherited in an autosomal dominant manner.2 Their febrile seizures can be associated with abnormalities in their temporal lobes,3,4 including bilamination of the dentate gyrus and other findings conventionally associated with temporal lobe epilepsy, implicating potential epilepsy-related mechanisms.5 Further evaluation of this emerging epilepsy-related phenotype has led to the identification of genetic variants in SCN1A and other epilepsy-associated genes,6,7 moving SUDC away from being considered an unexplained phenomenon to one where the working hypothesis includes a role for genetic predisposition and epilepsy-like mechanisms in the deaths, even without an established history of epilepsy. Nonetheless, because the terminal events of these seemingly healthy children are unexpected and unobserved, the clinical manifestations of whatever underlying vulnerabilities exist-generally discovered posthumously-remain a matter of speculation.
Collapse
Affiliation(s)
- Richard D Goldstein
- From the Departments of Pediatrics (R.D.G.) and Neurology (A.P.), Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Annapurna Poduri
- From the Departments of Pediatrics (R.D.G.) and Neurology (A.P.), Boston Children's Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
4
|
Gould L, Reid CA, Rodriguez AJ, Devinsky O. Video Analyses of Sudden Unexplained Deaths in Toddlers. Neurology 2024; 102:e208038. [PMID: 38175965 PMCID: PMC11097764 DOI: 10.1212/wnl.0000000000208038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/13/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND AND OBJECTIVES More than 2,900 US children aged younger than 4 years die from unknown causes each year, accounting for more than 219,000 life years lost annually. They are mostly sleep-related and unwitnessed with unremarkable autopsies, limiting our understanding of death mechanisms. We sought to understand potential mechanisms of death by evaluating videos of sudden deaths in toddlers. METHODS In our registry of 301 sudden unexplained child deaths, a series of 7 consecutively enrolled cases with home video recordings of the child's last sleep period were independently assessed by 8 physicians for video quality, movement, and sound. RESULTS Four boys and 3 girls (13-27 months at death) with terminal videos shared similar demographic features to the 293 other registry cases without video recordings. Five video recordings were continuous and 2 were triggered by sound or motion. Two lacked audio. All continuous recordings included a terminal convulsive event lasting 8-50 seconds; 4 children survived for >2.5 minutes postconvulsion. Among discontinuous videos, time lapses limited review; 1 suggested a convulsive event. Six were prone with face down, and 1 had autopsy evidence of airway obstruction. Primary cardiac arrhythmias were not supported; all 7 children had normal cardiac pathology and whole-exome sequencing identified no known cardiac disease variants. DISCUSSION Audio-visual recordings in 7 toddlers with unexplained sudden deaths strongly implicate that deaths were related to convulsive seizures, suggesting that many unexplained sleep-related deaths may result from seizures.
Collapse
Affiliation(s)
- Laura Gould
- From the NYU Grossman School of Medicine (L.G., C.-A.R., A.J.R., O.D.), and NYU Comprehensive Epilepsy Center (L.G., C.-A.R., A.J.R., O.D.), New York
| | - Codi-Ann Reid
- From the NYU Grossman School of Medicine (L.G., C.-A.R., A.J.R., O.D.), and NYU Comprehensive Epilepsy Center (L.G., C.-A.R., A.J.R., O.D.), New York
| | - Alcibiades J Rodriguez
- From the NYU Grossman School of Medicine (L.G., C.-A.R., A.J.R., O.D.), and NYU Comprehensive Epilepsy Center (L.G., C.-A.R., A.J.R., O.D.), New York
| | - Orrin Devinsky
- From the NYU Grossman School of Medicine (L.G., C.-A.R., A.J.R., O.D.), and NYU Comprehensive Epilepsy Center (L.G., C.-A.R., A.J.R., O.D.), New York
| |
Collapse
|
5
|
Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Karthik F, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Faulkner M, MacLeod HM, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. Genome Med 2024; 16:13. [PMID: 38229148 PMCID: PMC10792876 DOI: 10.1186/s13073-024-01284-w] [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: 02/22/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. METHODS The SDY Case Registry is a National Institutes of Health/Centers for Disease Control and Prevention surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases < 20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015 to 2019. The cohort included 211 children (median age 0.33 year; range 0-20 years), determined to have died suddenly and unexpectedly and from whom DNA biospecimens for DNA extractions and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex- and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy, and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, pathogenic and likely pathogenic genetic variation was identified using a Bayesian-based artificial intelligence (AI) tool. RESULTS The SDY cohort was 43% European, 29% African, 3% Asian, 16% Hispanic, and 9% with mixed ancestries and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy, or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, potentially damaging variants in epilepsy, cardiomyopathy, and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. CONCLUSIONS While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
Collapse
Affiliation(s)
- Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Lorenzo L Pesce
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Gregory Webster
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Mark W Russell
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah S Geisler
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Samuel D Kearns
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Felix Karthik
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan P Etheridge
- Division of Pediatric Cardiology, University of Utah, Salt Lake City, UT, USA
| | - Tanner O Monroe
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tess D Pottinger
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Prince J Kannankeril
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Darlene Fountain
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Kristin M Burns
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
6
|
Krygier M, Pietruszka M, Zawadzka M, Sawicka A, Lemska A, Limanówka M, Żurek J, Talaśka-Liczbik W, Mazurkiewicz-Bełdzińska M. Next-generation sequencing testing in children with epilepsy reveals novel clinical, diagnostic and therapeutic implications. Front Genet 2024; 14:1300952. [PMID: 38250573 PMCID: PMC10796783 DOI: 10.3389/fgene.2023.1300952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction: Epilepsy is one of the commonest diseases in children, characterized by extensive phenotypic and genetic heterogeneity. This study was conducted to determine the diagnostic utility and to identify novel clinical and therapeutic implications of genetic testing in pediatric patients with epilepsy. Methods: Large multigene panel and/or exome sequencing was performed in 127 unrelated Polish and Ukrainian patients with suspected monogenic epilepsy. Diagnostic yields were presented for five phenotypic subgroups, distinguished by seizure type, electroencephalographic abnormalities, anti-seizure treatment response, and neurodevelopmental deficits. Results: A definite molecular diagnosis was established in 46 out of 127 cases (36%). Alterations in six genes were detected in more than one patient: SCN1A, MECP2, KCNT1, KCNA2, PCDH19, SLC6A1, STXBP1, and TPP1, accounting for 48% of positive cases. 4/46 cases (8.7%) were mosaic for the variant. Although the highest rates of positive diagnoses were identified in children with developmental delay and generalized seizures (17/41, 41%) and in developmental end epileptic encephalopathies (16/40, 40%), a monogenic etiology was also frequently detected in patients with solely focal seizures (10/28, 36%). Molecular diagnosis directly influenced anti-seizure management in 15/46 cases. Conclusion: This study demonstrates the high diagnostic and therapeutic utility of large panel testing in childhood epilepsies irrespective of seizure types. Copy number variations and somatic mosaic variants are important disease-causing factors, pointing the need for comprehensive genetic testing in all unexplained cases. Pleiotropy is a common phenomenon contributing to the growing phenotypic complexity of single-gene epilepsies.
Collapse
Affiliation(s)
- Magdalena Krygier
- *Correspondence: Magdalena Krygier, ; Maria Mazurkiewicz-Bełdzińska,
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Gould L, Delavale V, Plovnick C, Wisniewski T, Devinsky O. Are brief febrile seizures benign? A systematic review and narrative synthesis. Epilepsia 2023; 64:2539-2549. [PMID: 37466925 DOI: 10.1111/epi.17720] [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: 03/16/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Febrile seizures affect 2%-5% of U.S. children and are considered benign although associated with an increased risk of epilepsy and, rarely, with sudden unexplained death. We compared rates of mortality, neurodevelopmental disorders, and neuropathology in young children with simple and complex febrile seizures to healthy controls. We systematically reviewed studies of 3- to 72-month-old children with simple or complex febrile seizures ≤30 min. We searched studies with outcome measures on mortality, neurodevelopment, or neuropathology through July 18, 2022. Bias risk was assessed per study design. Each outcome measure was stratified by study design. PROSPERO registration is CRD42022361645. Twenty-six studies met criteria reporting mortality (11), neurodevelopment (11), and neuropathology (13), including 2665 children with febrile seizures and 1206 seizure-free controls. Study designs varied: 15 cohort, 2 cross-sectional, 3 case-control, 5 series, and 1 case report. Mortality outcomes showed stark contrasts. Six cohort studies following children after febrile seizure (n = 1348) reported no deaths, whereas four child death series and 1 case report identified 24.1% (108/449) deaths associated with simple (n = 104) and complex (n = 3) febrile seizures ≤30 min. Minor hippocampal histopathological anomalies were common in sudden deaths with or without febrile seizure history. Most electroencephalography (EEG) studies were normal. Neuroimaging studies suggested increased right hippocampal volumes. When present, neurodevelopmental problems usually preexisted febrile-seizure onset. Risk bias was medium or high in 95% (18/19) of cohort and case-control studies vs medium to low across remaining study designs. Research on outcomes after simple or brief complex febrile seizures is limited. Cohort studies suffered from inadequate sample size, bias risk, and limited follow-up durations to make valid conclusions on mortality, neurodevelopment, and neuropathology. Sudden death registries, focused on a very small percentage of all cases, strongly suggest that simple febrile seizures are associated with increased mortality. Although most children with febrile seizures have favorable outcomes, longer-term prospective studies are needed.
Collapse
Affiliation(s)
- Laura Gould
- Comprehensive Epilepsy Center, NYU Langone Health, New York, New York, USA
- Department of Neurology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
| | - Victoria Delavale
- Comprehensive Epilepsy Center, NYU Langone Health, New York, New York, USA
- Department of Neurology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
| | - Caitlin Plovnick
- Health Sciences Library, NYU Grossman School of Medicine, New York, New York, USA
| | - Thomas Wisniewski
- Department of Neurology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
- Center for Cognitive Neurology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
- Department of Psychiatry, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, NYU Langone Health, New York, New York, USA
- Department of Neurology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
- Department of Psychiatry, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
| |
Collapse
|
8
|
Wojcik MH, Poduri AH, Holm IA, MacRae CA, Goldstein RD. The fundamental need for unifying phenotypes in sudden unexpected pediatric deaths. Front Med (Lausanne) 2023; 10:1166188. [PMID: 37332751 PMCID: PMC10273404 DOI: 10.3389/fmed.2023.1166188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/03/2023] [Indexed: 06/20/2023] Open
Abstract
A definitive, authoritative approach to evaluate the causes of unexpected, and ultimately unexplained, pediatric deaths remains elusive, relegating final conclusions to diagnoses of exclusion in the vast majority of cases. Research into unexplained pediatric deaths has focused primarily on sudden infant deaths (under 1 year of age) and led to the identification of several potential, albeit incompletely understood, contributory factors: nonspecific pathology findings, associations with sleep position and environment that may not be uniformly relevant, and the elucidation of a role for serotonin that is practically difficult to estimate in any individual case. Any assessment of progress in this field must also acknowledge the failure of current approaches to substantially decrease mortality rates in decades. Furthermore, potential commonalities with pediatric deaths across a broader age spectrum have not been widely considered. Recent epilepsy-related observations and genetic findings, identified post-mortem in both infants and children who died suddenly and unexpectedly, suggest a role for more intense and specific phenotyping efforts as well as an expanded role for genetic and genomic evaluation. We therefore present a new approach to reframe the phenotype in sudden unexplained deaths in the pediatric age range, collapsing many distinctions based on arbitrary factors (such as age) that have previously guided research in this area, and discuss its implications for the future of postmortem investigation.
Collapse
Affiliation(s)
- Monica H. Wojcik
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Annapurna H. Poduri
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Ingrid A. Holm
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Calum A. MacRae
- Harvard Medical School, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Richard D. Goldstein
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| |
Collapse
|
9
|
Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Etheridge FK, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, MacLeod H, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.27.23287711. [PMID: 37034657 PMCID: PMC10081419 DOI: 10.1101/2023.03.27.23287711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. Methods The SDY Case Registry is a National Institutes of Health/Centers for Disease Control surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases <20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015-2019. The cohort included 211 children (mean age 1 year; range 0-20 years), determined to have died suddenly and unexpectedly and in whom DNA biospecimens and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex-and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, genetic variation predicted to be damaging was identified using a Bayesian-based artificial intelligence (AI) tool. Results The SDY cohort was 42% European, 30% African, 17% Hispanic, and 11% with mixed ancestries, and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, damaging variants in epilepsy, cardiomyopathy and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. Conclusions While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort, and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
Collapse
|
10
|
Leitner DF, William C, Faustin A, Askenazi M, Kanshin E, Snuderl M, McGuone D, Wisniewski T, Ueberheide B, Gould L, Devinsky O. Proteomic differences in hippocampus and cortex of sudden unexplained death in childhood. Acta Neuropathol 2022; 143:585-599. [PMID: 35333953 PMCID: PMC8953962 DOI: 10.1007/s00401-022-02414-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/01/2022]
Abstract
Sudden unexplained death in childhood (SUDC) is death of a child over 1 year of age that is unexplained after review of clinical history, circumstances of death, and complete autopsy with ancillary testing. Multiple etiologies may cause SUDC. SUDC and sudden unexpected death in epilepsy (SUDEP) share clinical and pathological features, suggesting some similarities in mechanism of death and possible abnormalities in hippocampus and cortex. To identify molecular signaling pathways, we performed label-free quantitative mass spectrometry on microdissected frontal cortex, hippocampal dentate gyrus (DG), and cornu ammonis (CA1-3) in SUDC (n = 19) and pediatric control cases (n = 19) with an explained cause of death. At a 5% false discovery rate (FDR), we found differential expression of 660 proteins in frontal cortex, 170 in DG, and 57 in CA1-3. Pathway analysis of altered proteins identified top signaling pathways associated with activated oxidative phosphorylation (p = 6.3 × 10-15, z = 4.08) and inhibited EIF2 signaling (p = 2.0 × 10-21, z = - 2.56) in frontal cortex, and activated acute phase response in DG (p = 8.5 × 10-6, z = 2.65) and CA1-3 (p = 4.7 × 10-6, z = 2.00). Weighted gene correlation network analysis (WGCNA) of clinical history indicated that SUDC-positive post-mortem virology (n = 4/17) had the most significant module in each brain region, with the top most significant associated with decreased mRNA metabolic processes (p = 2.8 × 10-5) in frontal cortex. Additional modules were associated with clinical history, including fever within 24 h of death (top: increased mitochondrial fission in DG, p = 1.8 × 10-3) and febrile seizure history (top: decreased small molecule metabolic processes in frontal cortex, p = 8.8 × 10-5) in all brain regions, neuropathological hippocampal findings in the DG (top: decreased focal adhesion, p = 1.9 × 10-3). Overall, cortical and hippocampal protein changes were present in SUDC cases and some correlated with clinical features. Our studies support that proteomic studies of SUDC cohorts can advance our understanding of the pathogenesis of these tragedies and may inform the development of preventive strategies.
Collapse
|
11
|
Koh HY, Haghighi A, Keywan C, Alexandrescu S, Plews-Ogan E, Haas EA, Brownstein CA, Vargas SO, Haynes RL, Berry GT, Holm IA, Poduri AH, Goldstein RD. Genetic Determinants of Sudden Unexpected Death in Pediatrics. Genet Med 2022; 24:839-850. [PMID: 35027292 PMCID: PMC9164313 DOI: 10.1016/j.gim.2021.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
PURPOSE This study aimed to evaluate genetic contributions to sudden unexpected death in pediatrics (SUDP). METHODS We phenotyped and performed exome sequencing for 352 SUDP cases. We analyzed variants in 294 "SUDP genes" with mechanisms plausibly related to sudden death. In a subset of 73 cases with parental data (trios), we performed exome-wide analyses and conducted cohort-wide burden analyses. RESULTS In total, we identified likely contributory variants in 37 of 352 probands (11%). Analysis of SUDP genes identified pathogenic/likely pathogenic variants in 12 of 352 cases (SCN1A, DEPDC5 [2], GABRG2, SCN5A [2], TTN [2], MYBPC3, PLN, TNNI3, and PDHA1) and variants of unknown significance-favor-pathogenic in 17 of 352 cases. Exome-wide analyses of the 73 cases with family data additionally identified 4 de novo pathogenic/likely pathogenic variants (SCN1A [2], ANKRD1, and BRPF1) and 4 de novo variants of unknown significance-favor-pathogenic. Comparing cases with controls, we demonstrated an excess burden of rare damaging SUDP gene variants (odds ratio, 2.94; 95% confidence interval, 2.37-4.21) and of exome-wide de novo variants in the subset of 73 with trio data (odds ratio, 3.13; 95% confidence interval, 1.91-5.16). CONCLUSION We provide strong evidence for a role of genetic factors in SUDP, involving both candidate genes and novel genes for SUDP and expanding phenotypes of disease genes not previously associated with sudden death.
Collapse
Affiliation(s)
- Hyun Yong Koh
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, MA
| | - Alireza Haghighi
- Department of Genetics, Harvard Medical School, Boston, MA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Christine Keywan
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA
| | - Sanda Alexandrescu
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Erin Plews-Ogan
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Elisabeth A Haas
- Department of Research, Rady Children's Hospital-San Diego, San Diego, CA
| | - Catherine A Brownstein
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Sara O Vargas
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Robin L Haynes
- Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Gerard T Berry
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ingrid A Holm
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Annapurna H Poduri
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology, Harvard Medical School, Boston, MA
| | - Richard D Goldstein
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA.
| |
Collapse
|
12
|
Fischer FP, Kasture AS, Hummel T, Sucic S. Molecular and Clinical Repercussions of GABA Transporter 1 Variants Gone Amiss: Links to Epilepsy and Developmental Spectrum Disorders. Front Mol Biosci 2022; 9:834498. [PMID: 35295842 PMCID: PMC7612498 DOI: 10.3389/fmolb.2022.834498] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
The human γ-aminobutyric acid (GABA) transporter 1 (hGAT-1) is the first member of the solute carrier 6 (SLC6) protein superfamily. GAT-1 (SLC6A1) is one of the main GABA transporters in the central nervous system. Its principal physiological role is retrieving GABA from the synapse into neurons and astrocytes, thus swiftly terminating neurotransmission. GABA is a key inhibitory neurotransmitter and shifts in GABAergic signaling can lead to pathological conditions, from anxiety and epileptic seizures to schizophrenia. Point mutations in the SLC6A1 gene frequently give rise to epilepsy, intellectual disability or autism spectrum disorders in the afflicted individuals. The mechanistic routes underlying these are still fairly unclear. Some loss-of-function variants impair the folding and intracellular trafficking of the protein (thus retaining the transporter in the endoplasmic reticulum compartment), whereas others, despite managing to reach their bona fide site of action at the cell surface, nonetheless abolish GABA transport activity (plausibly owing to structural/conformational defects). Whatever the molecular culprit(s), the physiological aftermath transpires into the absence of functional transporters, which in turn perturbs GABAergic actions. Dozens of mutations in the kin SLC6 family members are known to exhort protein misfolding. Such events typically elicit severe ailments in people, e.g., infantile parkinsonism-dystonia or X-linked intellectual disability, in the case of dopamine and creatine transporters, respectively. Flaws in protein folding can be rectified by small molecules known as pharmacological and/or chemical chaperones. The search for such apt remedies calls for a systematic investigation and categorization of the numerous disease-linked variants, by biochemical and pharmacological means in vitro (in cell lines and primary neuronal cultures) and in vivo (in animal models). We here give special emphasis to the utilization of the fruit fly Drosophila melanogaster as a versatile model in GAT-1-related studies. Jointly, these approaches can portray indispensable insights into the molecular factors underlying epilepsy, and ultimately pave the way for contriving efficacious therapeutic options for patients harboring pathogenic mutations in hGAT-1.
Collapse
Affiliation(s)
- Florian P. Fischer
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ameya S. Kasture
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Thomas Hummel
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
13
|
Ding J, Li X, Tian H, Wang L, Guo B, Wang Y, Li W, Wang F, Sun T. SCN1A Mutation-Beyond Dravet Syndrome: A Systematic Review and Narrative Synthesis. Front Neurol 2022; 12:743726. [PMID: 35002916 PMCID: PMC8739186 DOI: 10.3389/fneur.2021.743726] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background:SCN1A is one of the most common epilepsy genes. About 80% of SCN1A gene mutations cause Dravet syndrome (DS), which is a severe and catastrophic epileptic encephalopathy. More than 1,800 mutations have been identified in SCN1A. Although it is known that SCN1A is the main cause of DS and genetic epilepsy with febrile seizures plus (GEFS+), there is a dearth of information on the other related diseases caused by mutations of SCN1A. Objective: The aim of this study is to systematically review the literature associated with SCN1A and other non-DS-related disorders. Methods: We searched PubMed and SCOPUS for all the published cases related to gene mutations of SCN1A until October 20, 2021. The results reported by each study were summarized narratively. Results: The PubMed and SCOPUS search yielded 2,889 items. A total of 453 studies published between 2005 and 2020 met the final inclusion criteria. Overall, 303 studies on DS, 93 on GEFS+, three on Doose syndrome, nine on the epilepsy of infancy with migrating focal seizures (EIMFS), six on the West syndrome, two on the Lennox–Gastaut syndrome (LGS), one on the Rett syndrome, seven on the nonsyndromic epileptic encephalopathy (NEE), 19 on hemiplegia migraine, six on autism spectrum disorder (ASD), two on nonepileptic SCN1A-related sudden deaths, and two on the arthrogryposis multiplex congenital were included. Conclusion: Aside from DS, SCN1A also causes other epileptic encephalopathies, such as GEFS+, Doose syndrome, EIMFS, West syndrome, LGS, Rett syndrome, and NEE. In addition to epilepsy, hemiplegic migraine, ASD, sudden death, and arthrogryposis multiplex congenital can also be caused by mutations of SCN1A.
Collapse
Affiliation(s)
- Jiangwei Ding
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Xinxiao Li
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyan Tian
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Department of Neurosurgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Baorui Guo
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| | - Yangyang Wang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Department of Neurosurgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Wenchao Li
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Department of Neurosurgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Feng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Sun
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, China
| |
Collapse
|
14
|
Mei Y, Zhang H, Zhang Z. Comparing Clinical and Genetic Characteristics of De Novo and Inherited COL1A1/COL1A2 Variants in a Large Chinese Cohort of Osteogenesis Imperfecta. Front Endocrinol (Lausanne) 2022; 13:935905. [PMID: 35909573 PMCID: PMC9329653 DOI: 10.3389/fendo.2022.935905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Nearly 85%-90% of osteogenesis imperfecta (OI) cases are caused by autosome dominant mutations of COL1A1 and COL1A2 genes, of which de novo mutations cover a large proportion, whereas their characteristics remain to be elucidated. This study aims to compare the differences in clinical and genetic characteristics of de novo and inherited COL1A1/COL1A2 mutations of OI, assess the average paternal and maternal age at conception in de novo mutations, and research the rate of nonpenetrance in inherited mutations. MATERIALS AND METHODS A retrospective comparison between de novo and inherited mutations was performed among 135 OI probands with COL1A1/COL1A2 mutations. Mutational analyses of all probands and their family members were completed by Sanger sequencing. A new clinical scoring system was developed to assess the clinical severity of OI quantitatively. RESULTS A total of 51 probands (37.78%) with de novo mutations and 84 probands (62.22%) with inherited mutations were grouped by the results of the parental gene verification. The proportion of clinical type III (P<0.001) and clinical scores (P<0.001) were significantly higher in de novo mutations. Missense mutations covered a slightly higher proportion of de novo COL1A1 mutations (46.34%) compared with inherited COL1A1 mutations (33.33%), however, lacking a significant difference (P=0.1923). The mean BMD Z/T-score at the lumbar spine in de novo mutations was -2.3 ± 1.5, lower than inherited mutations (-1.7 ± 1.8), but lacking statistical significance (P=0.0742). There was no significant difference between the two groups in OI-related phenotypes (like fracture frequency, blue sclera, and hearing loss) and biochemical indexes. In de novo mutations, the average paternal and maternal age at conception was 29.2 (P<0.05) and 26.8 (P<0.0001), respectively, which were significantly younger than the average gestational age of the population. Additionally, 98.04% of pedigrees (50/51) with de novo mutations were spontaneous conception. The rate of nonpenetrance of parents with pathogenic variants in the inherited mutation group was 25.64% (20/78). CONCLUSIONS Our data revealed that the proportion of clinical type III and clinical scores were significantly higher in de novo mutations than in inherited mutations, demonstrating that de novo mutations are more damaging because they have not undergone purifying selection.
Collapse
Affiliation(s)
| | - Hao Zhang
- *Correspondence: Zhenlin Zhang, ; Hao Zhang,
| | | |
Collapse
|
15
|
De novo mutations in childhood cases of sudden unexplained death that disrupt intracellular Ca2+ regulation. Proc Natl Acad Sci U S A 2021; 118:2115140118. [PMID: 34930847 PMCID: PMC8719874 DOI: 10.1073/pnas.2115140118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 01/04/2023] Open
Abstract
Approximately 400 United States children 1 y of age and older die suddenly from unexplained causes annually. We studied whole-exome sequence data from 124 “trios” (decedent child and living parents) to identify genetic risk factors. Nonsynonymous mutations, mostly de novo (present in child but absent in both biological parents), were highly enriched in genes associated with cardiac and seizure disorders relative to controls, and contributed to 9% of deaths. We found significant overtransmission of loss-of-function or pathogenic missense variants in cardiac and seizure disorder genes. Most pathogenic variants were de novo in origin, highlighting the importance of trio studies. Many of these pathogenic de novo mutations altered a protein network regulating calcium-related excitability at submembrane junctions in cardiomyocytes and neurons. Sudden unexplained death in childhood (SUDC) is an understudied problem. Whole-exome sequence data from 124 “trios” (decedent child, living parents) was used to test for excessive de novo mutations (DNMs) in genes involved in cardiac arrhythmias, epilepsy, and other disorders. Among decedents, nonsynonymous DNMs were enriched in genes associated with cardiac and seizure disorders relative to controls (odds ratio = 9.76, P = 2.15 × 10−4). We also found evidence for overtransmission of loss-of-function (LoF) or previously reported pathogenic variants in these same genes from heterozygous carrier parents (11 of 14 transmitted, P = 0.03). We identified a total of 11 SUDC proband genotypes (7 de novo, 1 transmitted parental mosaic, 2 transmitted parental heterozygous, and 1 compound heterozygous) as pathogenic and likely contributory to death, a genetic finding in 8.9% of our cohort. Two genes had recurrent missense DNMs, RYR2 and CACNA1C. Both RYR2 mutations are pathogenic (P = 1.7 × 10−7) and were previously studied in mouse models. Both CACNA1C mutations lie within a 104-nt exon (P = 1.0 × 10−7) and result in slowed L-type calcium channel inactivation and lower current density. In total, six pathogenic DNMs can alter calcium-related regulation of cardiomyocyte and neuronal excitability at a submembrane junction, suggesting a pathway conferring susceptibility to sudden death. There was a trend for excess LoF mutations in LoF intolerant genes, where ≥1 nonhealthy sample in denovo-db has a similar variant (odds ratio = 6.73, P = 0.02); additional uncharacterized genetic causes of sudden death in children might be discovered with larger cohorts.
Collapse
|
16
|
Chmielewska JJ, Burkardt D, Granadillo JL, Slaugh R, Morgan S, Rotenberg J, Keren B, Mignot C, Escobar L, Turnpenny P, Zuteck M, Seaver LH, Ploski R, Dziembowska M, Wynshaw-Boris A, Adegbola A. PTPN4 germline variants result in aberrant neurodevelopment and growth. HGG ADVANCES 2021; 2:100033. [PMID: 34527963 PMCID: PMC8439436 DOI: 10.1016/j.xhgg.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/31/2021] [Indexed: 11/29/2022] Open
Abstract
Protein-tyrosine phosphatases (PTPs) are pleomorphic regulators of eukaryotic cellular responses to extracellular signals that function by modulating the phosphotyrosine of specific proteins. A handful of PTPs have been implicated in germline and somatic human disease. Using exome sequencing, we identified missense and truncating variants in PTPN4 in six unrelated individuals with varying degrees of intellectual disability or developmental delay. The variants occurred de novo in all five subjects in whom segregation analysis was possible. Recurring features include postnatal growth deficiency or excess, seizures, and, less commonly, structural CNS, heart, or skeletal anomalies. PTPN4 is a widely expressed protein tyrosine phosphatase that regulates neuronal cell homeostasis by protecting neurons against apoptosis. We suggest that pathogenic variants in PTPN4 confer risk for growth and cognitive abnormalities in humans.
Collapse
Affiliation(s)
- Joanna J. Chmielewska
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
- Laboratory of Molecular Basis of Synaptic Plasticity, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Deepika Burkardt
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
| | - Jorge Luis Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Boris Keren
- Département de Génétique, APHP, Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Département de Génétique, APHP, Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Luis Escobar
- Medical Genetics and Neurodevelopmental Center, Peyton Manning Children’s Hospital, Indianapolis, IN, USA
| | - Peter Turnpenny
- University of Exeter Medical School and Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Melissa Zuteck
- Medical Genetics and Genomics, Spectrum Health/Helen Devos Children’s Hospital, Grand Rapids, MI, USA
| | - Laurie H. Seaver
- Medical Genetics and Genomics, Spectrum Health/Helen Devos Children’s Hospital, Grand Rapids, MI, USA
- Department of Pediatrics and Human Development, Michigan State College of Human Medicine, Grand Rapids, MI, USA
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Magdalena Dziembowska
- Laboratory of Molecular Basis of Synaptic Plasticity, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Anthony Wynshaw-Boris
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
| | - Abidemi Adegbola
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
- Department of Psychiatry, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
17
|
Pires G, Leitner D, Drummond E, Kanshin E, Nayak S, Askenazi M, Faustin A, Friedman D, Debure L, Ueberheide B, Wisniewski T, Devinsky O. Proteomic differences in the hippocampus and cortex of epilepsy brain tissue. Brain Commun 2021; 3:fcab021. [PMID: 34159317 DOI: 10.1093/braincomms/fcab021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Epilepsy is a common neurological disorder affecting over 70 million people worldwide, with a high rate of pharmaco-resistance, diverse comorbidities including progressive cognitive and behavioural disorders, and increased mortality from direct (e.g. sudden unexpected death in epilepsy, accidents, drowning) or indirect effects of seizures and therapies. Extensive research with animal models and human studies provides limited insights into the mechanisms underlying seizures and epileptogenesis, and these have not translated into significant reductions in pharmaco-resistance, morbidities or mortality. To help define changes in molecular signalling networks associated with seizures in epilepsy with a broad range of aetiologies, we examined the proteome of brain samples from epilepsy and control cases. Label-free quantitative mass spectrometry was performed on the hippocampal cornu ammonis 1-3 region (CA1-3), frontal cortex and dentate gyrus microdissected from epilepsy and control cases (n = 14/group). Epilepsy cases had significant differences in the expression of 777 proteins in the hippocampal CA1 - 3 region, 296 proteins in the frontal cortex and 49 proteins in the dentate gyrus in comparison to control cases. Network analysis showed that proteins involved in protein synthesis, mitochondrial function, G-protein signalling and synaptic plasticity were particularly altered in epilepsy. While protein differences were most pronounced in the hippocampus, similar changes were observed in other brain regions indicating broad proteomic abnormalities in epilepsy. Among the most significantly altered proteins, G-protein subunit beta 1 (GNB1) was one of the most significantly decreased proteins in epilepsy in all regions studied, highlighting the importance of G-protein subunit signalling and G-protein-coupled receptors in epilepsy. Our results provide insights into common molecular mechanisms underlying epilepsy across various aetiologies, which may allow for novel targeted therapeutic strategies.
Collapse
Affiliation(s)
- Geoffrey Pires
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA.,Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Dominique Leitner
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Faculty of Medicine and Health, Brain and Mind Centre and School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Shruti Nayak
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Manor Askenazi
- Biomedical Hosting LLC, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Arline Faustin
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel Friedman
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Ludovic Debure
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.,Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
18
|
Keywan C, Poduri AH, Goldstein RD, Holm IA. Genetic Factors Underlying Sudden Infant Death Syndrome. APPLICATION OF CLINICAL GENETICS 2021; 14:61-76. [PMID: 33623412 PMCID: PMC7894824 DOI: 10.2147/tacg.s239478] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/24/2021] [Indexed: 12/28/2022]
Abstract
Sudden Infant Death syndrome (SIDS) is a diagnosis of exclusion. Decades of research have made steady gains in understanding plausible mechanisms of terminal events. Current evidence suggests SIDS includes heterogeneous biological conditions, such as metabolic, cardiac, neurologic, respiratory, and infectious conditions. Here we review genetic studies that address each of these areas in SIDS cases and cohorts, providing a broad view of the genetic underpinnings of this devastating phenomenon. The current literature has established a role for monogenic genetic causes of SIDS mortality in a subset of cases. To expand upon our current knowledge of disease-causing genetic variants in SIDS cohorts and their mechanisms, future genetic studies may employ functional assessments of implicated variants, broader genetic tests, and the inclusion of parental genetic data and family history information.
Collapse
Affiliation(s)
- Christine Keywan
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna H Poduri
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Richard D Goldstein
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ingrid A Holm
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of Genetics and Genomics, Department of Pediatrics, and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA
| |
Collapse
|
19
|
Harowitz J, Crandall L, McGuone D, Devinsky O. Seizure-related deaths in children: The expanding spectrum. Epilepsia 2021; 62:570-582. [PMID: 33586153 PMCID: PMC7986159 DOI: 10.1111/epi.16833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022]
Abstract
Although seizures are common in children, they are often overlooked as a potential cause of death. Febrile and nonfebrile seizures can be fatal in children with or without an epilepsy diagnosis and may go unrecognized by parents or physicians. Sudden unexpected infant deaths, sudden unexplained death in childhood, and sudden unexpected death in epilepsy share clinical, neuropathological, and genetic features, including male predominance, unwitnessed deaths, death during sleep, discovery in the prone position, hippocampal abnormalities, and variants in genes regulating cardiac and neuronal excitability. Additionally, epidemiological studies reveal that miscarriages are more common among individuals with a personal or family history of epilepsy, suggesting that some fetal losses may result from epileptic factors. The spectrum of seizure-related deaths in pediatrics is wide and underappreciated; accurately estimating this mortality and understanding its mechanism in children is critical to developing effective education and interventions to prevent these tragedies.
Collapse
Affiliation(s)
- Jenna Harowitz
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Laura Crandall
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, New York, USA.,SUDC Foundation, Herndon, Virginia, USA
| | - Declan McGuone
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, New York, USA
| |
Collapse
|
20
|
Bhat S, El-Kasaby A, Freissmuth M, Sucic S. Functional and Biochemical Consequences of Disease Variants in Neurotransmitter Transporters: A Special Emphasis on Folding and Trafficking Deficits. Pharmacol Ther 2020; 222:107785. [PMID: 33310157 PMCID: PMC7612411 DOI: 10.1016/j.pharmthera.2020.107785] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/02/2020] [Indexed: 01/30/2023]
Abstract
Neurotransmitters, such as γ-aminobutyric acid, glutamate, acetyl choline, glycine and the monoamines, facilitate the crosstalk within the central nervous system. The designated neurotransmitter transporters (NTTs) both release and take up neurotransmitters to and from the synaptic cleft. NTT dysfunction can lead to severe pathophysiological consequences, e.g. epilepsy, intellectual disability, or Parkinson’s disease. Genetic point mutations in NTTs have recently been associated with the onset of various neurological disorders. Some of these mutations trigger folding defects in the NTT proteins. Correct folding is a prerequisite for the export of NTTs from the endoplasmic reticulum (ER) and the subsequent trafficking to their pertinent site of action, typically at the plasma membrane. Recent studies have uncovered some of the key features in the molecular machinery responsible for transporter protein folding, e.g., the role of heat shock proteins in fine-tuning the ER quality control mechanisms in cells. The therapeutic significance of understanding these events is apparent from the rising number of reports, which directly link different pathological conditions to NTT misfolding. For instance, folding-deficient variants of the human transporters for dopamine or GABA lead to infantile parkinsonism/dystonia and epilepsy, respectively. From a therapeutic point of view, some folding-deficient NTTs are amenable to functional rescue by small molecules, known as chemical and pharmacological chaperones.
Collapse
Affiliation(s)
- Shreyas Bhat
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria.
| |
Collapse
|
21
|
McGuone D, Crandall LG, Devinsky O. Sudden Unexplained Death in Childhood: A Neuropathology Review. Front Neurol 2020; 11:582051. [PMID: 33178125 PMCID: PMC7596260 DOI: 10.3389/fneur.2020.582051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Sudden Unexplained Death in Childhood (SUDC) is the unexpected death of a child over age 12 months that remains unexplained after a thorough case investigation, including review of the child's medical history, circumstances of death, a complete autopsy and ancillary testing (1). First defined in 2005, SUDC cases are more often male, with death occurring during a sleep period, being found prone, peak winter incidence, associated with febrile seizure history in ~28% of cases and mild pathologic changes insufficient to explain the death (1, 2). There has been little progress in understanding the causes of SUDC and no progress in prevention. Despite reductions in sudden unexpected infant death (SUID) and other causes of mortality in childhood, the rate of SUDC has increased during the past two decades (3-5). In Ireland, SUID deaths were cut in half from 1994 to 2008 while SUDC deaths more than doubled (4). Surveillance issues, including lack of standardized certification practices, affect our understanding of the true magnitude of unexplained child deaths. Mechanisms underlying SUDC, like SUID, remain largely speculative. Limited and inconsistent evidence implicates abnormalities in brainstem autonomic and serotonergic nuclei, critical for arousal, cardiorespiratory control, and reflex responses to life-threatening hypoxia or hypercarbia in sleep (6). Abnormalities in medullary serotonergic neurons and receptors, as well as cardiorespiratory brainstem nuclei occur in some SUID cases, but have never been studied in SUDC. Retrospective, small SUDC studies with non-standardized methodologies most often demonstrate minor hippocampal abnormalities, as well as focal cortical dysplasia and dysgenesis of the brainstem and cerebellum. The significance of these findings to SUDC pathogenesis remains unclear with some investigators and forensic pathologists labeling these findings as normal variants, or potential causes of SUDC. The development of preventive strategies will require a greater understanding of underlying mechanisms.
Collapse
Affiliation(s)
- Declan McGuone
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Laura G Crandall
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, NY, United States.,SUDC Foundation, Herndon, VA, United States
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, NY, United States
| |
Collapse
|
22
|
Crandall LG, Lee JH, Friedman D, Lear K, Maloney K, Pinckard JK, Lin P, Andrew T, Roman K, Landi K, Jarrell H, Williamson AK, Downs JCU, Pinneri K, William C, Maleszewski JJ, Reichard RR, Devinsky O. Evaluation of Concordance Between Original Death Certifications and an Expert Panel Process in the Determination of Sudden Unexplained Death in Childhood. JAMA Netw Open 2020; 3:e2023262. [PMID: 33125496 PMCID: PMC7599447 DOI: 10.1001/jamanetworkopen.2020.23262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE The true incidence of sudden unexplained death in childhood (SUDC), already the fifth leading category of death among toddlers by current US Centers for Disease Control and Prevention estimates, is potentially veiled by the varied certification processes by medicolegal investigative offices across the United States. OBJECTIVE To evaluate the frequency of SUDC incidence, understand its epidemiology, and assess the consistency of death certification among medical examiner and coroner offices in the US death investigation system. DESIGN, SETTING, AND PARTICIPANTS In this case series, 2 of 13 forensic pathologists (FPs) conducted masked reviews of 100 cases enrolled in the SUDC Registry and Research Collaborative (SUDCRRC). Children who died aged 11 months to 18 years from 36 US states, Canada, and the United Kingdom had been posthumously enrolled in the SUDCRRC by family members from 2014 to 2017. Comprehensive data from medicolegal investigative offices, clinical offices, and family members were reviewed. Data analysis was conducted from December 2014 to June 2020. MAIN OUTCOMES AND MEASURES Certified cause of death (COD) characterized as explained (accidental or natural) or unexplained, as determined by SUDCRRC masked review process. RESULTS In this study of 100 cases of SUDC (mean [SD] age, 32.1 [31.8] months; 58 [58.0%] boys; 82 [82.0%] White children; 92 [92.0%] from the United States), the original pathologist certified 43 cases (43.0%) as explained COD and 57 (57.0%) as unexplained COD. The SUDCRRC review process led to the following certifications: 16 (16.0%) were explained, 7 (7.0%) were undetermined because of insufficient data, and 77 (77.0%) were unexplained. Experts disagreed with the original COD in 40 cases (40.0%). These data suggest that SUDC incidence is higher than the current Centers for Disease Control and Prevention estimate (ie, 392 deaths in 2018). CONCLUSIONS AND RELEVANCE To our knowledge, this is the first comprehensive masked forensic pathology review process of sudden unexpected pediatric deaths, and it suggests that SUDC may often go unrecognized in US death investigations. Some unexpected pediatric deaths may be erroneously attributed to a natural or accidental COD, negatively affecting surveillance, research, public health funding, and medical care of surviving family members. To further address the challenges of accurate and consistent death certification in SUDC, future studies are warranted.
Collapse
Affiliation(s)
| | - Joyce H. Lee
- NYU Grossman School of Medicine, New York, New York
| | | | - Kelly Lear
- Arapahoe County Coroner’s Office, Centennial, Colorado
| | - Katherine Maloney
- Erie County Medical Examiner's Office, Buffalo, New York
- University at Buffalo School of Medicine, Buffalo, New York
| | | | | | - Thomas Andrew
- White Mountain Forensic Consulting Services, Concord, New Hampshire
| | | | | | | | | | | | - Kathy Pinneri
- Montgomery County Forensic Services Department, Conroe, Texas
| | | | | | | | | |
Collapse
|
23
|
Menezes LFS, Sabiá Júnior EF, Tibery DV, Carneiro LDA, Schwartz EF. Epilepsy-Related Voltage-Gated Sodium Channelopathies: A Review. Front Pharmacol 2020; 11:1276. [PMID: 33013363 PMCID: PMC7461817 DOI: 10.3389/fphar.2020.01276] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022] Open
Abstract
Epilepsy is a disease characterized by abnormal brain activity and a predisposition to generate epileptic seizures, leading to neurobiological, cognitive, psychological, social, and economic impacts for the patient. There are several known causes for epilepsy; one of them is the malfunction of ion channels, resulting from mutations. Voltage-gated sodium channels (NaV) play an essential role in the generation and propagation of action potential, and malfunction caused by mutations can induce irregular neuronal activity. That said, several genetic variations in NaV channels have been described and associated with epilepsy. These mutations can affect channel kinetics, modifying channel activation, inactivation, recovery from inactivation, and/or the current window. Among the NaV subtypes related to epilepsy, NaV1.1 is doubtless the most relevant, with more than 1500 mutations described. Truncation and missense mutations are the most observed alterations. In addition, several studies have already related mutated NaV channels with the electrophysiological functioning of the channel, aiming to correlate with the epilepsy phenotype. The present review provides an overview of studies on epilepsy-associated mutated human NaV1.1, NaV1.2, NaV1.3, NaV1.6, and NaV1.7.
Collapse
Affiliation(s)
- Luis Felipe Santos Menezes
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Elias Ferreira Sabiá Júnior
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Lilian Dos Anjos Carneiro
- Faculdade de Medicina, Centro Universitário Euro Americano, Brasília, Brazil.,Faculdade de Medicina, Centro Universitário do Planalto Central, Brasília, Brazil
| | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| |
Collapse
|
24
|
Rochtus AM, Goldstein RD, Holm IA, Brownstein CA, Pérez‐Palma E, Haynes R, Lal D, Poduri AH. The role of sodium channels in sudden unexpected death in pediatrics. Mol Genet Genomic Med 2020; 8:e1309. [PMID: 32449611 PMCID: PMC7434613 DOI: 10.1002/mgg3.1309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sudden Unexpected Death in Pediatrics (SUDP) is a tragic event, likely caused by the complex interaction of multiple factors. The presence of hippocampal abnormalities in many children with SUDP suggests that epilepsy-related mechanisms may contribute to death, similar to Sudden Unexplained Death in Epilepsy. Because of known associations between the genes SCN1A and SCN5A and sudden death, and shared mechanisms and patterns of expression in genes encoding many voltage-gated sodium channels (VGSCs), we hypothesized that individuals dying from SUDP have pathogenic variants across the entire family of cardiac arrhythmia- and epilepsy-associated VGSC genes. METHODS To address this hypothesis, we evaluated whole-exome sequencing data from infants and children with SUDP for variants in VGSC genes, reviewed the literature for all SUDP-associated variants in VGSCs, applied a novel paralog analysis to all variants, and evaluated all variants according to American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS In our cohort of 73 cases of SUDP, we assessed 11 variants as pathogenic in SCN1A, SCN1B, and SCN10A, genes with long-standing disease associations, and in SCN3A, SCN4A, and SCN9A, VGSC gene paralogs with more recent disease associations. From the literature, we identified 82 VGSC variants in SUDP cases. Pathogenic variants clustered at conserved amino acid sites intolerant to variation across the VGSC genes, which is unlikely to occur in the general population (p < .0001). For 54% of variants previously reported in literature, we identified conflicting evidence regarding pathogenicity when applying ACMG criteria and modern population data. CONCLUSION We report variants in several VGSC genes in cases with SUDP, involving both arrhythmia- and epilepsy-associated genes. Accurate variant assessment as well as future studies are essential for an improved understanding of the contribution of sodium channel-related variants to SUDP.
Collapse
Affiliation(s)
- Anne M. Rochtus
- Department of NeurologyBoston Children's Hospital and Harvard Medical SchoolBostonMAUSA
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Department of PediatricsUniversity of LeuvenLeuvenBelgium
| | - Richard D. Goldstein
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Department of PediatricsBoston Children’s Hospital and Harvard Medical SchoolBostonMAUSA
| | - Ingrid A. Holm
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Department of PediatricsBoston Children’s Hospital and Harvard Medical SchoolBostonMAUSA
- Department of MedicineDivision of Genetics and Genomics and the Manton Center for Orphan Disease ResearchBoston Children's HospitalBostonMAUSA
| | - Catherine A. Brownstein
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Department of PediatricsBoston Children’s Hospital and Harvard Medical SchoolBostonMAUSA
- Department of MedicineDivision of Genetics and Genomics and the Manton Center for Orphan Disease ResearchBoston Children's HospitalBostonMAUSA
| | - Eduardo Pérez‐Palma
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOHUSA
- Cologne Center for GenomicsUniversity of CologneCologneGermany
| | - Robin Haynes
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Department of PathologyBoston Children’s Hospital and Harvard Medical SchoolBostonMAUSA
| | - Dennis Lal
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOHUSA
- Cologne Center for GenomicsUniversity of CologneCologneGermany
- Stanley Center for Psychiatric ResearchBroad Institute of Harvard and MITCambridgeMAUSA
| | - Annapurna H. Poduri
- Department of NeurologyBoston Children's Hospital and Harvard Medical SchoolBostonMAUSA
- Robert’s Program on Sudden Death in PediatricsBoston Children’s HospitalBostonMAUSA
- Stanley Center for Psychiatric ResearchBroad Institute of Harvard and MITCambridgeMAUSA
| |
Collapse
|
25
|
Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
Collapse
Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| |
Collapse
|
26
|
Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 2020; 22:1768-1776. [PMID: 32655138 PMCID: PMC7606563 DOI: 10.1038/s41436-020-0897-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases. Methods: We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents. Results: Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples. Conclusion: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.
Collapse
Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nina G Xie
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ed Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
| |
Collapse
|
27
|
Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med 2020; 12:49. [PMID: 32460841 PMCID: PMC7254727 DOI: 10.1186/s13073-020-00746-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. METHODS Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. RESULTS The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. CONCLUSIONS In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
Collapse
Affiliation(s)
- Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Luis Zapata
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
28
|
Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
Collapse
Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
29
|
Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
Collapse
Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
30
|
Concurrent pathogenic variants in SLC6A1/NOTCH1/PRIMPOL genes in a Chinese patient with myoclonic-atonic epilepsy, mild aortic valve stenosis and high myopia. BMC MEDICAL GENETICS 2020; 21:93. [PMID: 32375772 PMCID: PMC7203802 DOI: 10.1186/s12881-020-01035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/27/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pathogenic SLC6A1 variants have been reported in patients with myoclonic-atonic epilepsy (MAE). NOTCH1, encoding a member of the Notch family of proteins, is known to be associated with aortic valve disease. The PRIMPOL variant has only been identified in Chinese patients with high myopia. Exome sequencing analysis now allows the simultaneous detection of multiple genetic etiologies for patients with complicated clinical features. However, the presence of three Mendelian disorders in one patient supported by their respective pathogenic variants and clinical phenotypes is very rare. CASE PRESENTATION Here, we report a 4-year-old Chinese boy who presented with MAE, delayed language, borderline intellectual disability (ID), mildly impaired social skills and attention deficit hyperactivity disorder (ADHD). He also had mild aortic valve stenosis and high myopia. Using whole-exome sequencing (WES), we identified three variants: (1) SLC6A1, NM_003042.4: c.881-883del (p.Phe294del), (2) NOTCH1, NM_017617.5:c.1100-2A > G and (3) PRIMPOL, NM_152683.4:c.265 T > G (p.Tyr89Asp). Parental Sanger sequencing confirmed that SLC6A1 and NOTCH1 variants were de novo, whereas the PRIMPOL variant was inherited from the father who also had high myopia. Furthermore, the PRIMPOL variant was absent from the genomes of the paternal grandparents, and thus was also a de novo event in the family. All three variants are classified as pathogenic. CONCLUSION The SLC6A1 variant could explain the features of MAE, delayed language, borderline ID, impaired social skills and ADHD in this patient, whereas the features of aortic valve stenosis and high myopia of the patient may be explained by variants in NOTCH1 and PRIMPOL, respectively. This case demonstrated the utility of exome sequencing in uncovering the multiple pathogenic variants in a patient with complicated phenotypes due to the blending of three Mendelian disorders.
Collapse
|
31
|
Matthews E, Balestrini S, Sisodiya SM, Hanna MG. Muscle and brain sodium channelopathies: genetic causes, clinical phenotypes, and management approaches. THE LANCET CHILD & ADOLESCENT HEALTH 2020; 4:536-547. [PMID: 32142633 DOI: 10.1016/s2352-4642(19)30425-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/29/2019] [Accepted: 12/12/2019] [Indexed: 01/26/2023]
Abstract
Voltage-gated sodium channels are essential for excitability of skeletal muscle fibres and neurons. An increasing number of disabling or fatal paediatric neurological disorders linked to mutations of voltage-gated sodium channel genes are recognised. Muscle phenotypes include episodic paralysis, myotonia, neonatal hypotonia, respiratory compromise, laryngospasm or stridor, congenital myasthenia, and myopathy. Evidence suggests a possible link between sodium channel dysfunction and sudden infant death. Increasingly recognised phenotypes of brain sodium channelopathies include several epilepsy disorders and complex encephalopathies. Together, these early-onset muscle and brain phenotypes have a substantial morbidity and a considerable mortality. Important advances in understanding the pathophysiological mechanisms underlying these channelopathies have helped to identify effective targeted therapies. The availability of effective treatments underlines the importance of increasing clinical awareness and the need to achieve a precise genetic diagnosis. In this Review, we describe the expanded range of phenotypes of muscle and brain sodium channelopathies and the underlying knowledge regarding mechanisms of sodium channel dysfunction. We also outline a diagnostic approach and review the available treatment options.
Collapse
Affiliation(s)
- Emma Matthews
- Department of Neuromuscular Diseases, Medical Research Council Centre for Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK.
| | - Simona Balestrini
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Buckinghamshire, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Buckinghamshire, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, Medical Research Council Centre for Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
| |
Collapse
|
32
|
McGuone D, Leitner D, William C, Faustin A, Leelatian N, Reichard R, Shepherd TM, Snuderl M, Crandall L, Wisniewski T, Devinsky O. Neuropathologic Changes in Sudden Unexplained Death in Childhood. J Neuropathol Exp Neurol 2020; 79:336-346. [PMID: 31995186 PMCID: PMC7036658 DOI: 10.1093/jnen/nlz136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/14/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022] Open
Abstract
Sudden unexplained death in childhood (SUDC) affects children >1-year-old whose cause of death remains unexplained following comprehensive case investigation and is often associated with hippocampal abnormalities. We prospectively performed systematic neuropathologic investigation in 20 SUDC cases, including (i) autopsy data and comprehensive ancillary testing, including molecular studies, (ii) ex vivo 3T MRI and extensive histologic brain samples, and (iii) blinded neuropathology review by 2 board-certified neuropathologists. There were 12 girls and 8 boys; median age at death was 33.3 months. Twelve had a history of febrile seizures, 85% died during apparent sleep and 80% in prone position. Molecular testing possibly explained 3 deaths and identified genetic mutations in TNNI3, RYR2, and multiple chromosomal aberrations. Hippocampal abnormalities most often affected the dentate gyrus (altered thickness, irregular configuration, and focal lack of granule cells), and had highest concordance between reviewers. Findings were identified with similar frequencies in cases with and without molecular findings. Number of seizures did not correlate with hippocampal findings. Hippocampal alterations were the most common finding on histological review but were also found in possibly explained deaths. The significance and specificity of hippocampal findings is unclear as they may result from seizures, contribute to seizure pathogenesis, or be an unrelated phenomenon.
Collapse
Affiliation(s)
- Declan McGuone
- From the Department of Pathology, Yale School of Medicine, New haven, Connecticut
| | - Dominique Leitner
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, New York
| | - Christopher William
- Department of Neurology
- Department of Pathology, NYU Langone Health and School of Medicine, New York, New York
| | | | - Nalin Leelatian
- From the Department of Pathology, Yale School of Medicine, New haven, Connecticut
| | - Ross Reichard
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Matija Snuderl
- Department of Pathology, NYU Langone Health and School of Medicine, New York, New York
| | - Laura Crandall
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, New York
- Sudden Unexplained Death in Childhood Foundation, Cedar Grove, New Jersey
| | - Thomas Wisniewski
- Department of Neurology
- Center for Cognitive Neurology, and Psychiatry, NYU Langone Health and School of Medicine, New York, New York
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, New York
| |
Collapse
|
33
|
Scheffer IE, Nabbout R. SCN1A‐related phenotypes: Epilepsy and beyond. Epilepsia 2019; 60 Suppl 3:S17-S24. [DOI: 10.1111/epi.16386] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ingrid E. Scheffer
- Departments of Medicine and Paediatrics Austin Health and Royal Children’s Hospital Florey and Murdoch Children’s Research Institute The University of Melbourne Melbourne VIC Australia
| | - Rima Nabbout
- Reference Centre for Rare Epilepsies Department of Paediatric Neurology Necker Enfants Malades Hospital Imagine Institute U1163 Paris Descartes University Paris France
| |
Collapse
|
34
|
Wang J, Liu Z, Bellen HJ, Yamamoto S. Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. J Vis Exp 2019:10.3791/59542. [PMID: 31475990 PMCID: PMC7401700 DOI: 10.3791/59542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Through whole-exome/genome sequencing, human geneticists identify rare variants that segregate with disease phenotypes. To assess if a specific variant is pathogenic, one must query many databases to determine whether the gene of interest is linked to a genetic disease, whether the specific variant has been reported before, and what functional data is available in model organism databases that may provide clues about the gene's function in human. MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) is a one-stop data collection tool for human genes and variants and their orthologous genes in seven model organisms including in mouse, rat, zebrafish, fruit fly, nematode worm, fission yeast, and budding yeast. In this Protocol, we provide an overview of what MARRVEL can be used for and discuss how different datasets can be used to assess whether a variant of unknown significance (VUS) in a known disease-causing gene or a variant in a gene of uncertain significance (GUS) may be pathogenic. This protocol will guide a user through searching multiple human databases simultaneously starting with a human gene with or without a variant of interest. We also discuss how to utilize data from OMIM, ExAC/gnomAD, ClinVar, Geno2MP, DGV and DECHIPHER. Moreover, we illustrate how to interpret a list of ortholog candidate genes, expression patterns, and GO terms in model organisms associated with each human gene. Furthermore, we discuss the value protein structural domain annotations provided and explain how to use the multiple species protein alignment feature to assess whether a variant of interest affects an evolutionarily conserved domain or amino acid. Finally, we will discuss three different use-cases of this website. MARRVEL is an easily accessible open access website designed for both clinical and basic researchers and serves as a starting point to design experiments for functional studies.
Collapse
Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Baylor College of Medicine; Medical Scientist Training Program, Baylor College of Medicine
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Neuroscience, Baylor College of Medicine; Howard Hughes Medical Institute, Baylor College of Medicine
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Neuroscience, Baylor College of Medicine;
| |
Collapse
|
35
|
Vidal S, Xiol C, Pascual-Alonso A, O'Callaghan M, Pineda M, Armstrong J. Genetic Landscape of Rett Syndrome Spectrum: Improvements and Challenges. Int J Mol Sci 2019; 20:ijms20163925. [PMID: 31409060 PMCID: PMC6719047 DOI: 10.3390/ijms20163925] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that primarily affects females, resulting in severe cognitive and physical disabilities, and is one of the most prevalent causes of intellectual disability in females. More than fifty years after the first publication on Rett syndrome, and almost two decades since the first report linking RTT to the MECP2 gene, the research community's effort is focused on obtaining a better understanding of the genetics and the complex biology of RTT and Rett-like phenotypes without MECP2 mutations. Herein, we review the current molecular genetic studies, which investigate the genetic causes of RTT or Rett-like phenotypes which overlap with other genetic disorders and document the swift evolution of the techniques and methodologies employed. This review also underlines the clinical and genetic heterogeneity of the Rett syndrome spectrum and provides an overview of the RTT-related genes described to date, many of which are involved in epigenetic gene regulation, neurotransmitter action or RNA transcription/translation. Finally, it discusses the importance of including both phenotypic and genetic diagnosis to provide proper genetic counselling from a patient's perspective and the appropriate treatment.
Collapse
Affiliation(s)
- Silvia Vidal
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Clara Xiol
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Ainhoa Pascual-Alonso
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - M O'Callaghan
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- Neurology Service, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mercè Pineda
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
| | - Judith Armstrong
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain.
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain.
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, 08950 Barcelona, Spain.
| |
Collapse
|
36
|
Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. Nat Commun 2019; 10:2985. [PMID: 31278258 PMCID: PMC6611863 DOI: 10.1038/s41467-019-11059-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mosaic genetic variants can have major clinical impact. We systematically analyse trio exome sequence data from 4,293 probands from the DDD Study with severe developmental disorders for pathogenic postzygotic mosaicism (PZM) in the child or a clinically-unaffected parent, and use ultrahigh-depth sequencing to validate candidate mosaic variants. We observe that levels of mosaicism for small genetic variants are usually equivalent in both saliva and blood and ~3% of causative de novo mutations exhibit PZM; this is an important observation, as the sibling recurrence risk is extremely low. We identify parental PZM in 21 trios (0.5% of trios), resulting in a substantially increased sibling recurrence risk in future pregnancies. Together, these forms of mosaicism account for 40 (1%) diagnoses in our cohort. Likely child-PZM mutations occur equally on both parental haplotypes, and the penetrance of detectable mosaic pathogenic variants overall is likely to be less than half that of constitutive variants.
Collapse
|
37
|
Low-level mosaicism in tuberous sclerosis complex: prevalence, clinical features, and risk of disease transmission. Genet Med 2019; 21:2639-2643. [PMID: 31160751 DOI: 10.1038/s41436-019-0562-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/22/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To examine the prevalence and spectrum of mosaic variant allele frequency (MVAF) in tuberous sclerosis complex (TSC) patients with low-level mosaicism and correlate genetic findings with clinical features and transmission risk. METHODS Massively parallel sequencing was performed on 39 mosaic TSC patients with 170 different tissue samples. RESULTS TSC mosaic patients (MVAF: 0-10%, median 1.7% in blood DNA) had a milder and distinct clinical phenotype in comparison with other TSC series, with similar facial angiofibromas (92%) and kidney angiomyolipomas (83%), and fewer seizures, cortical tubers, and multiple other manifestations (p < 0.0001 for six features). MVAF of TSC1/TSC2 pathogenic variants was highly variable in different tissue samples. Remarkably, skin lesions were the most reliable tissue for variant identification, and 6 of 39 (15%) patients showed no evidence of the variant in blood. Semen analysis showed absence of the variant in 3 of 5 mosaic men. The expected distribution of MVAF in comparison with that observed here suggests that there is a considerable number of individuals with low-level mosaicism for a TSC2 pathogenic variant who are not recognized clinically. CONCLUSION Our findings provide information on variability in MVAF and risk of transmission that has broad implications for other mosaic genetic disorders.
Collapse
|
38
|
Jansen S, van der Werf IM, Innes AM, Afenjar A, Agrawal PB, Anderson IJ, Atwal PS, van Binsbergen E, van den Boogaard MJ, Castiglia L, Coban-Akdemir ZH, van Dijck A, Doummar D, van Eerde AM, van Essen AJ, van Gassen KL, Guillen Sacoto MJ, van Haelst MM, Iossifov I, Jackson JL, Judd E, Kaiwar C, Keren B, Klee EW, Klein Wassink-Ruiter JS, Meuwissen ME, Monaghan KG, de Munnik SA, Nava C, Ockeloen CW, Pettinato R, Racher H, Rinne T, Romano C, Sanders VR, Schnur RE, Smeets EJ, Stegmann APA, Stray-Pedersen A, Sweetser DA, Terhal PA, Tveten K, VanNoy GE, de Vries PF, Waxler JL, Willing M, Pfundt R, Veltman JA, Kooy RF, Vissers LELM, de Vries BBA. De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Eur J Hum Genet 2019; 27:738-746. [PMID: 30679813 DOI: 10.1038/s41431-018-0292-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/07/2018] [Accepted: 09/25/2018] [Indexed: 01/15/2023] Open
Abstract
Determining pathogenicity of genomic variation identified by next-generation sequencing techniques can be supported by recurrent disruptive variants in the same gene in phenotypically similar individuals. However, interpretation of novel variants in a specific gene in individuals with mild-moderate intellectual disability (ID) without recognizable syndromic features can be challenging and reverse phenotyping is often required. We describe 24 individuals with a de novo disease-causing variant in, or partial deletion of, the F-box only protein 11 gene (FBXO11, also known as VIT1 and PRMT9). FBXO11 is part of the SCF (SKP1-cullin-F-box) complex, a multi-protein E3 ubiquitin-ligase complex catalyzing the ubiquitination of proteins destined for proteasomal degradation. Twenty-two variants were identified by next-generation sequencing, comprising 2 in-frame deletions, 11 missense variants, 1 canonical splice site variant, and 8 nonsense or frameshift variants leading to a truncated protein or degraded transcript. The remaining two variants were identified by array-comparative genomic hybridization and consisted of a partial deletion of FBXO11. All individuals had borderline to severe ID and behavioral problems (autism spectrum disorder, attention-deficit/hyperactivity disorder, anxiety, aggression) were observed in most of them. The most relevant common facial features included a thin upper lip and a broad prominent space between the paramedian peaks of the upper lip. Other features were hypotonia and hyperlaxity of the joints. We show that de novo variants in FBXO11 cause a syndromic form of ID. The current series show the power of reverse phenotyping in the interpretation of novel genetic variances in individuals who initially did not appear to have a clear recognizable phenotype.
Collapse
Affiliation(s)
- Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse M van der Werf
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada
| | - Alexandra Afenjar
- Centre de Référence Déficiences Intellectuelles de Causes Rares, 75013, Paris, France.,APHP, GHUEP, Hôpital Armand Trousseau, Centre de Référence 'Malformations et maladies congénitales du cervelet', 75012, Paris, France
| | - Pankaj B Agrawal
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ilse J Anderson
- The University of Tennessee Genetics Center, Knoxville, TN, 37920, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Marie-José van den Boogaard
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Lucia Castiglia
- Laboratory of Medical Genetics, Oasi Research Institute, 94018, Troina, Italy
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anke van Dijck
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Diane Doummar
- APHP, Service de Neurologie pédiatrique, Hôpital Armand Trousseau, Paris, France.,Sorbonne Université,GRC ConCer-LD, AP-HP, Hôpital Trousseau, Paris, France.,Service de neuropediatrie, Hôpital Trousseau, 26 avenue du dr Arnold Netter, 75012, Paris, France
| | - Albertien M van Eerde
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Koen L van Gassen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | - Mieke M van Haelst
- Department of Clinical Genetics, VU University Medical Center, 1081 HV, Amsterdam, The Netherlands
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,New York Genome Center, New York, NY, 10013, USA
| | - Jessica L Jackson
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Elizabeth Judd
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA.,Invitae, 1400 16th Street, San Francisco, CA, 94103, USA
| | - Boris Keren
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Marije E Meuwissen
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | | | - Sonja A de Munnik
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caroline Nava
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France.,INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Université de Paris 06, 75013, Paris, France
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Rosa Pettinato
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Hilary Racher
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada.,Impact Genetics, 1100 Bennett Road, Bowmanville, ON, L1C 3K5, Canada
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Corrado Romano
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Victoria R Sanders
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Ann and Robert H Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL, 60611, USA
| | | | - Eric J Smeets
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Pb 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Grace E VanNoy
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Petra F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Marcia Willing
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - R Frank Kooy
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
| |
Collapse
|
39
|
Liu Z, Zhang N, Zhang Y, Du Y, Zhang T, Li Z, Wu J, Wang X. Prioritized High-Confidence Risk Genes for Intellectual Disability Reveal Molecular Convergence During Brain Development. Front Genet 2018; 9:349. [PMID: 30279698 PMCID: PMC6153320 DOI: 10.3389/fgene.2018.00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 01/09/2023] Open
Abstract
Dissecting the genetic susceptibility to intellectual disability (ID) based on de novo mutations (DNMs) will aid our understanding of the neurobiological and genetic basis of ID. In this study, we identify 63 high-confidence ID genes with q-values < 0.1 based on four background DNM rates and coding DNM data sets from multiple sequencing cohorts. Bioinformatic annotations revealed a higher burden of these 63 ID genes in FMRP targets and CHD8 targets, and these genes show evolutionary constraint against functional genetic variation. Moreover, these ID risk genes were preferentially expressed in the cortical regions from the early fetal to late mid-fetal stages. In particular, a genome-wide weighted co-expression network analysis suggested that ID genes tightly converge onto two biological modules (M1 and M2) during human brain development. Functional annotations showed specific enrichment of chromatin modification and transcriptional regulation for M1 and synaptic function for M2, implying the divergent etiology of the two modules. In addition, we curated 12 additional strong ID risk genes whose molecular interconnectivity with known ID genes (q-values < 0.3) was greater than random. These findings further highlight the biological convergence of ID risk genes and help improve our understanding of the genetic architecture of ID.
Collapse
Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yu Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
40
|
Mattison KA, Butler KM, Inglis GAS, Dayan O, Boussidan H, Bhambhani V, Philbrook B, da Silva C, Alexander JJ, Kanner BI, Escayg A. SLC6A1 variants identified in epilepsy patients reduce γ-aminobutyric acid transport. Epilepsia 2018; 59:e135-e141. [PMID: 30132828 DOI: 10.1111/epi.14531] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022]
Abstract
Previous reports have identified SLC6A1 variants in patients with generalized epilepsies, such as myoclonic-atonic epilepsy and childhood absence epilepsy. However, to date, none of the identified SLC6A1 variants has been functionally tested for an effect on GAT-1 transporter activity. The purpose of this study was to determine the incidence of SLC6A1 variants in 460 unselected epilepsy patients and to evaluate the impact of the identified variants on γ-aminobutyric acid (GABA)transport. Targeted resequencing was used to screen 460 unselected epilepsy patients for variants in SLC6A1. Five missense variants, one in-frame deletion, one nonsense variant, and one intronic splice-site variant were identified, representing a 1.7% diagnostic yield. Using a [3 H]-GABA transport assay, the seven identified exonic variants were found to reduce GABA transport activity. A minigene splicing assay revealed that the splice-site variant disrupted canonical splicing of exon 9 in the mRNA transcript, leading to premature protein truncation. These findings demonstrate that SLC6A1 is an important contributor to childhood epilepsy and that reduced GAT-1 function is a common consequence of epilepsy-causing SLC6A1 variants.
Collapse
Affiliation(s)
- Kari A Mattison
- Department of Human Genetics, Emory University, Atlanta, Georgia.,Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia
| | - Kameryn M Butler
- Department of Human Genetics, Emory University, Atlanta, Georgia.,Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia
| | - George Andrew S Inglis
- Department of Human Genetics, Emory University, Atlanta, Georgia.,Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia
| | - Oshrat Dayan
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Hanna Boussidan
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Vikas Bhambhani
- Children's Hospitals and Clinics of Minnesota, Minneapolis, Minnesota
| | - Bryan Philbrook
- Department of Pediatric Neurology, Emory University, Atlanta, Georgia
| | | | - John J Alexander
- Department of Human Genetics, Emory University, Atlanta, Georgia.,EGL Genetics, Tucker, Georgia
| | - Baruch I Kanner
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Andrew Escayg
- Department of Human Genetics, Emory University, Atlanta, Georgia.,Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia
| |
Collapse
|
41
|
Abstract
Genetic mosaicism arises when a zygote harbors two or more distinct genotypes, typically due to de novo, somatic mutation during embryogenesis. The clinical manifestations largely depend on the differentiation status of the mutated cell; earlier mutations target pluripotent cells and generate more widespread disease affecting multiple organ systems. If gonadal tissue is spared-as in somatic genomic mosaicism-the mutation and its effects are limited to the proband, whereas mosaicism also affecting the gametes, such as germline or gonosomal mosaicism, is transmissible. Mosaicism is easily appreciated in cutaneous disorders, as phenotypically distinct mutant cells often give rise to lesions in patterns determined by the affected cell type. Genetic investigation of cutaneous mosaic disorders has identified pathways central to disease pathogenesis, revealing novel therapeutic targets. In this review, we discuss examples of cutaneous mosaicism, approaches to gene discovery in these disorders, and insights into molecular pathobiology that have potential for clinical translation.
Collapse
Affiliation(s)
- Young H Lim
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA; .,Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Zoe Moscato
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Keith A Choate
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA; .,Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| |
Collapse
|
42
|
Genetics of Epilepsy in the Era of Precision Medicine: Implications for Testing, Treatment, and Genetic Counseling. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0139-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
43
|
Brownstein CA, Goldstein RD, Thompson CH, Haynes RL, Giles E, Sheidley B, Bainbridge M, Haas EA, Mena OJ, Lucas J, Schaber B, Holm IA, George AL, Kinney HC, Poduri AH. SCN1A variants associated with sudden infant death syndrome. Epilepsia 2018; 59:e56-e62. [PMID: 29601086 DOI: 10.1111/epi.14055] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2018] [Indexed: 12/27/2022]
Abstract
We identified SCN1A variants in 2 infants who died of sudden infant death syndrome (SIDS) with hippocampal abnormalities from an exome sequencing study of 10 cases of SIDS but no history of seizures. One harbored SCN1A G682V, and the other had 2 SCN1A variants in cis: L1296M and E1308D, a variant previously associated with epilepsy. Functional evaluation in a heterologous expression system demonstrated partial loss of function for both G682V and the compound variant L1296M/E1308D. Our cases represent a novel association between SCN1A and SIDS, extending the SCN1A spectrum from epilepsy to SIDS. Our findings provide insights into SIDS and support genetic evaluation focused on epilepsy genes in SIDS.
Collapse
Affiliation(s)
- Catherine A Brownstein
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richard D Goldstein
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Division of General Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Christopher H Thompson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Robin L Haynes
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Emma Giles
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Beth Sheidley
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Elisabeth A Haas
- Department of Pathology, Rady Children's Hospital-San Diego, San Diego, CA, USA
| | - Othon J Mena
- Office of the Medical Examiner, County of San Diego Medical Examiner's Office, San Diego, CA, USA
| | - Jonathan Lucas
- Office of the Medical Examiner, County of San Diego Medical Examiner's Office, San Diego, CA, USA
| | - Bethann Schaber
- Office of the Medical Examiner, County of San Diego Medical Examiner's Office, San Diego, CA, USA
| | - Ingrid A Holm
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hannah C Kinney
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Annapurna H Poduri
- Robert's Program on Sudden Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
44
|
Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Front Genet 2018; 9:20. [PMID: 29467791 PMCID: PMC5808353 DOI: 10.3389/fgene.2018.00020] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS). For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.
Collapse
Affiliation(s)
- Paul Dunn
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| |
Collapse
|
45
|
Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
Collapse
|
46
|
Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
Collapse
Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
47
|
Johannesen KM, Gardella E, Linnankivi T, Courage C, de Saint Martin A, Lehesjoki AE, Mignot C, Afenjar A, Lesca G, Abi-Warde MT, Chelly J, Piton A, Merritt JL, Rodan LH, Tan WH, Bird LM, Nespeca M, Gleeson JG, Yoo Y, Choi M, Chae JH, Czapansky-Beilman D, Reichert SC, Pendziwiat M, Verhoeven JS, Schelhaas HJ, Devinsky O, Christensen J, Specchio N, Trivisano M, Weber YG, Nava C, Keren B, Doummar D, Schaefer E, Hopkins S, Dubbs H, Shaw JE, Pisani L, Myers CT, Tang S, Tang S, Pal DK, Millichap JJ, Carvill GL, Helbig KL, Mecarelli O, Striano P, Helbig I, Rubboli G, Mefford HC, Møller RS. Defining the phenotypic spectrum of SLC6A1 mutations. Epilepsia 2018; 59:389-402. [PMID: 29315614 DOI: 10.1111/epi.13986] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Pathogenic SLC6A1 variants were recently described in patients with myoclonic atonic epilepsy (MAE) and intellectual disability (ID). We set out to define the phenotypic spectrum in a larger cohort of SCL6A1-mutated patients. METHODS We collected 24 SLC6A1 probands and 6 affected family members. Four previously published cases were included for further electroclinical description. In total, we reviewed the electroclinical data of 34 subjects. RESULTS Cognitive development was impaired in 33/34 (97%) subjects; 28/34 had mild to moderate ID, with language impairment being the most common feature. Epilepsy was diagnosed in 31/34 cases with mean onset at 3.7 years. Cognitive assessment before epilepsy onset was available in 24/31 subjects and was normal in 25% (6/24), and consistent with mild ID in 46% (11/24) or moderate ID in 17% (4/24). Two patients had speech delay only, and 1 had severe ID. After epilepsy onset, cognition deteriorated in 46% (11/24) of cases. The most common seizure types were absence, myoclonic, and atonic seizures. Sixteen cases fulfilled the diagnostic criteria for MAE. Seven further patients had different forms of generalized epilepsy and 2 had focal epilepsy. Twenty of 31 patients became seizure-free, with valproic acid being the most effective drug. There was no clear-cut correlation between seizure control and cognitive outcome. Electroencephalography (EEG) findings were available in 27/31 patients showing irregular bursts of diffuse 2.5-3.5 Hz spikes/polyspikes-and-slow waves in 25/31. Two patients developed an EEG pattern resembling electrical status epilepticus during sleep. Ataxia was observed in 7/34 cases. We describe 7 truncating and 18 missense variants, including 4 recurrent variants (Gly232Val, Ala288Val, Val342Met, and Gly362Arg). SIGNIFICANCE Most patients carrying pathogenic SLC6A1 variants have an MAE phenotype with language delay and mild/moderate ID before epilepsy onset. However, ID alone or associated with focal epilepsy can also be observed.
Collapse
Affiliation(s)
- Katrine M Johannesen
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Elena Gardella
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Tarja Linnankivi
- Department of Child Neurology, Children's Hospital, Helsinki University Hospital Helsinki, University of Helsinki, Helsinki, Finland
| | - Carolina Courage
- The Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Research Programs Unit, Molecular Neurology and Neuroscience Center, Helsinki, Finland
| | - Anne de Saint Martin
- Department of Pediatrics, Pediatric Neurology, University Hospital of Strasbourg, Strasbourg, France.,Reference Center for Rare Epilepsies, Strasbourg, France
| | - Anna-Elina Lehesjoki
- The Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Research Programs Unit, Molecular Neurology and Neuroscience Center, Helsinki, Finland
| | - Cyril Mignot
- Department of Genetics, Center for Rare causes of Intellectual Disabilities and UPMC Research Group "Intellectual Disabilities and Autism", Paris, France
| | | | - Gaetan Lesca
- Departments of Genetics, Lyon University Hospitals, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,Lyon Neuroscience Research Center, CNRS UMRS5292, INSERM U1028, Lyon, France
| | - Marie-Thérèse Abi-Warde
- Department of Pediatrics, Pediatric Neurology, University Hospital of Strasbourg, Strasbourg, France.,Reference Center for Rare Epilepsies, Strasbourg, France
| | - Jamel Chelly
- Department of Translational Medicine and Neurogenetics, Institut Génétique Biologie Moléculaire Cellulaire (IGBMC), Illkirch, France.,Laboratory of Genetic Diagnosis, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institut Génétique Biologie Moléculaire Cellulaire (IGBMC), Illkirch, France.,Laboratory of Genetic Diagnosis, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - J Lawrence Merritt
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lance H Rodan
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Wen-Hann Tan
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Lynne M Bird
- Division of Genetics, Department of Pediatrics, Rady Children's Hospital San Diego, University of California San Diego, San Diego, CA, USA
| | - Mark Nespeca
- Division of Neurology, Rady Children's Hospital, University of California, San Diego, CA, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University School of Medicine, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University School of Medicine, Seoul, South Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University School of Medicine, Seoul, South Korea
| | | | | | - Manuela Pendziwiat
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Judith S Verhoeven
- Department of Neurology, Academic Center for Epileptology, Heeze, The Netherlands
| | - Helenius J Schelhaas
- Department of Neurology, Academic Center for Epileptology, Heeze, The Netherlands
| | | | - Jakob Christensen
- Department of Neurology, Aarhus University Hospital, Aarhus, Denmark
| | - Nicola Specchio
- Neurology Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marina Trivisano
- Neurology Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tüebingen, Tüebingen, Germany
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Sorbonne Universities, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Sorbonne Universities, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
| | - Diane Doummar
- Assistance Publique-Hôpitaux de Paris, Neuropediatric Services, Hospital Armand Trousseau, Paris, France
| | - Elise Schaefer
- Medical Genetics, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sarah Hopkins
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly Dubbs
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Jessica E Shaw
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Laura Pisani
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Shan Tang
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Deb K Pal
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - John J Millichap
- Epilepsy Center and Division of Neurology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gemma L Carvill
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Oriano Mecarelli
- Department of Neurology and Psychiatry, Neurophysiopathology and Neuromuscular Diseases, University of Sapeinza, Rome, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa 'G. Gaslini" Institute, Genova, Italy
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany.,Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Guido Rubboli
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,University of Copenhagen, Copenhagen, Denmark
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Rikke S Møller
- The Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
48
|
Weber YG, Biskup S, Helbig KL, Von Spiczak S, Lerche H. The role of genetic testing in epilepsy diagnosis and management. Expert Rev Mol Diagn 2017; 17:739-750. [PMID: 28548558 DOI: 10.1080/14737159.2017.1335598] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Epilepsy is a common neurological disorder characterized by recurrent unprovoked seizures. More than 500 epilepsy-associated genes have been described in the literature. Most of these genes play an important role in neuronal excitability, cortical development or synaptic transmission. A growing number of genetic variations have implications on diagnosis and prognostic or therapeutic advice in terms of a personalized medicine. Area covered: The review presents the different forms of genetic epilepsies with respect to their underlying genetic and functional pathophysiology and aims to give advice for recommended genetic testing. Moreover, it discusses ethical and legal guidelines, costs and technical limitations which should be considered. Expert commentary: Genetic testing is an important component in the diagnosis and treatment of many forms of epilepsy.
Collapse
Affiliation(s)
- Yvonne G Weber
- a Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research , University of Tübingen , Tubingen , Germany
| | - Saskia Biskup
- b CeGaT GmbH , Center for Genomics and Transcriptomics , Tübingen , Germany
| | - Katherine L Helbig
- c Division of Clinical Genomics , Ambry Genetics , Aliso Viejo , CA , USA
| | - Sarah Von Spiczak
- d Department of Neuropediatrics , University Medical Center Schleswig-Holstein, Christian Albrechts University , Kiel , Germany.,e Northern German Epilepsy Center for Children and Adolescents , Schwentinental-Raisdorf , Germany
| | - Holger Lerche
- a Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research , University of Tübingen , Tubingen , Germany
| |
Collapse
|
49
|
Mulkey SB, Ben-Zeev B, Nicolai J, Carroll JL, Grønborg S, Jiang YH, Joshi N, Kelly M, Koolen DA, Mikati MA, Park K, Pearl PL, Scheffer IE, Spillmann RC, Taglialatela M, Vieker S, Weckhuysen S, Cooper EC, Cilio MR. Neonatal nonepileptic myoclonus is a prominent clinical feature of KCNQ2 gain-of-function variants R201C and R201H. Epilepsia 2017; 58:436-445. [PMID: 28139826 DOI: 10.1111/epi.13676] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To analyze whether KCNQ2 R201C and R201H variants, which show atypical gain-of-function electrophysiologic properties in vitro, have a distinct clinical presentation and outcome. METHODS Ten children with heterozygous, de novo KCNQ2 R201C or R201H variants were identified worldwide, using an institutional review board (IRB)-approved KCNQ2 patient registry and database. We reviewed medical records and, where possible, interviewed parents and treating physicians using a structured, detailed phenotype inventory focusing on the neonatal presentation and subsequent course. RESULTS Nine patients had encephalopathy from birth and presented with prominent startle-like myoclonus, which could be triggered by sound or touch. In seven patients, electroencephalography (EEG) was performed in the neonatal period and showed a burst-suppression pattern. However, myoclonus did not have an EEG correlate. In many patients the paroxysmal movements were misdiagnosed as seizures. Seven patients developed epileptic spasms in infancy. In all patients, EEG showed a slow background and multifocal epileptiform discharges later in life. Other prominent features included respiratory dysfunction (perinatal respiratory failure and/or chronic hypoventilation), hypomyelination, reduced brain volume, and profound developmental delay. One patient had a later onset, and sequencing indicated that a low abundance (~20%) R201C variant had arisen by postzygotic mosaicism. SIGNIFICANCE Heterozygous KCNQ2 R201C and R201H gain-of-function variants present with profound neonatal encephalopathy in the absence of neonatal seizures. Neonates present with nonepileptic myoclonus that is often misdiagnosed and treated as seizures. Prognosis is poor. This clinical presentation is distinct from the phenotype associated with loss-of-function variants, supporting the value of in vitro functional screening. These findings suggest that gain-of-function and loss-of-function variants need different targeted therapeutic approaches.
Collapse
Affiliation(s)
- Sarah B Mulkey
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, U.S.A
| | - Bruria Ben-Zeev
- Department of Pediatrics, Sackler School of Medicine, Tel Hashomer, Israel
| | - Joost Nicolai
- Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - John L Carroll
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, U.S.A
| | - Sabine Grønborg
- Center for Rare Diseases, Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | - Yong-Hui Jiang
- Departments of Pediatrics and Neurobiology, Duke University Medical Center, Durham, North Carolina, U.S.A
| | - Nishtha Joshi
- Departments of Neurology, Neuroscience, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, U.S.A
| | - Megan Kelly
- Departments of Pediatrics and Neurobiology, Duke University Medical Center, Durham, North Carolina, U.S.A
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mohamad A Mikati
- Departments of Pediatrics and Neurobiology, Duke University Medical Center, Durham, North Carolina, U.S.A
| | - Kristen Park
- Department of Pediatrics, University of Colorado, Aurora, Colorado, U.S.A
| | - Phillip L Pearl
- Departments of Pediatrics and Neurology, Boston Children's Hospital, Boston, Massachusetts, U.S.A
| | | | - Rebecca C Spillmann
- Departments of Pediatrics and Neurobiology, Duke University Medical Center, Durham, North Carolina, U.S.A
| | - Maurizio Taglialatela
- Department of Neuroscience, University of Naples Federico II, Naples, Italy.,Department of Medicine and Health Sciences, University of Molise, Campobasso, Italy
| | | | - Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Edward C Cooper
- Departments of Neurology, Neuroscience, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, U.S.A
| | - Maria Roberta Cilio
- Departments of Neurology and Pediatrics, University of California San Francisco, San Francisco, California, U.S.A
| |
Collapse
|
50
|
Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
Collapse
Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| |
Collapse
|